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Here's a piece of practical advice: political science is a well-established field of study in which a PhD from a decent program will give you a good chance of obtaining a position both inside and outside of academia, whereas an interdisciplinary PhD like American Studies, or to a somewhat lesser extent Communications, will probably not make you a desirable candidate for any position.  American Studies, in particular, was a bit of a fad in the 1990s, and from what I've heard from those who had peers in this field those who received PhDs have largely struck out on the academic marketplace.  Really, you could make anything you are interested in researching in American Studies or Communications your focus in political science, and polisci covers a broader universe of topics in case you ever change your mind.  Accordingly, I would seriously think twice before even applying to an American Studies program.

Fwiw, if I could change one thing about my undergrad/grad training, I would have taken more political theory, or at any rate have read more of it outside of class. That others might deem it "irrelevant" is, well, "irrelevant." You're preparing yourself for a lifetime of scholarship in a particular discipline. Why one wouldn't want a solid background in the core texts of the field escapes me.

Oh right....you should be naming faculty (at least 2 I would say) who you would like to work with. But it seems less important to have a specific POI who you will work with, due to the nature of the discipline (you won't be working in someone's lab or generally jumping right on a research project). I would always name people whose work interests me, and meshes with mine-but I think in general decisions are not made by one person, and it is more about showing a general departmental fit, not targeting one person to work with.

Your undergraduate GPA is done; there's nothing you can do about it now, so there's no reason to worry about it excessively.  People with similar GPAs have gotten into top 10 programs, just don't shoot yourself in the foot by applying only to top ten programs.  Save enough cash to apply to a ton of programs (shoot for at least 20) that are spread out across the top 40, and you're bound to get at least a few good offers.  

The good news is that nearly two years is plenty of time to dramatically improve a file.  My two cents:
1) Your GRE needs to be significantly improved, and it's the worth investing the time needed to boost it up as high as possible.
2) Seriously try to publish something.  If you get an R&R from a decent journal, it will signal that you have an understanding of political science research is all about, and this will dispel any doubts about your coming from an MPA program. 

Also, why not consider PhD programs in public policy/administration too?  They generally require an MPA, which you will have, and the market for those is much better.  I'm assuming here that you have some interest in this study, since you're in an MPA program instead of a terminal MA.

I'm starting with Moore and Siegel's book 'A Mathematics Course for Political and Social Research' + the accompanying youtube videos. So far I have found them quite accesibile. I suppose I better have a look at the online OSU calc course.. I left all of this behind age 16, so I'm in for a real shock! Trying to get through it before July..

Tips:
1) Study calculus. Get as comfortable with derivatives as you can. If you find you have an aptitude for math, push forward to even a basic intro to matrix algebra. All of this will make a standard first year methods sequence easier.
 
2) Identify some data that you'd want someday to analyze. Methods are much easier to learn when you have an application.
 
3) Don't every use the phrase "undergrad cherry" again.
 
Congrats on your admission and best of luck.

Accepted into UVA off of the wait list in IR!!!!!! Unofficial email from the DGS last night. I'd been in contact with the department and they said they had more than one IR spot to fill, so don't lose hope.

With all due respect to the collective wisdom represented on these boards, to crowdsource this decision strikes me as crazy. You should be talking to your advisors, and to key faculty at the two excellent programs to which you've been admitted. Then follow recent placements at each and see which place does better placing graduates doing the kind of work you wish to do at the kinds of places you wish to work.
 
Congrats on your admission and best of luck.

Then be satisfied with nothing. That's the bottom line. You think you are entitled to things without making sacrifices or commitment. This isn't how things work in the real world.

ITT I see a lot of excuses and not a lot of action. Everything that is pointed out to you, you seem to reply back with some form of a caveat. 
 
For example:
 
- history has language requirements
- political science and other social sciences require quant training
- internships don't pay
- can't do X and Y because not in an honours program.
 
Sounds like a lot of excuses for your lack of motivation and/or laziness. Seriously. If you want something you have to jump through hoops and get the necessary skills and experience to get there. You are not entitled to anything. 
 
Personally, I have had to jump through a lot of hoops to get where I want to be academically, like learning languages when I am not particularly skilled or quick at them, taking and willing to improve my quant skills to succeed in political science, going to office hours countless times when talking to professors was once very intimidating for me, coming from a very untraditional and unacademic familial background and rising to the top of my respective cohorts on effort, ect. Life isn't all roses my friend, you need to do what you got to do to succeed if your desires are even somewhat ambitious. 

Oh! Also don't forget that professors leave universities. One way to choose would be to imagine all of your potential PIs took jobs elsewhere and then to decide which school would have more resources & infrastructure to support you.

I think (subfield-substantive) fit can be overweighed.  As a professional academic, you will have to get used to being off on your own to some degree; you might end up the only person at a university in your specific subfield. If you can find supportive faculty members capable of mentoring you in the methodological toolkit you need for your research program, I think that would go a long way even if your specific research interests do not overlap much.
 
Any indication of program desirability can be manipulated by strategic behavior, but I would at least focus on schools that make a strong effort to make you seem welcomed.  I've received emails from ten or so POIs at schools to which I have been accepted, and some put forth a great deal more effort in the recruitment process, mentioning parts of my writing sample they liked (and why), specific examples of students who have worked under them on related research projects and how their careers turned out, providing examples of papers they have co-written with students on similar topics, etc.  They're likely overselling, but making the effort to oversell should at least be loosely correlated with making a strong effort on the department's behalf elsewhere.  These are the sorts of people I feel comfortable committing to work with for several years based on asymmetric information.
 
Edit: I didn't mean to suggest that professors are largely disingenuous in their correspondence.  I just wanted to point out that even if you (wisely) assume that the program may not be as ideal for you in every way as it can sometimes be presented, you will still get incredibly valuable information from interacting with POIs.  When I'm deciding who I want to work under, I at least want someone who takes the time to strongly signal that he would be a good mentor.

I'm somebody who finished my PhD in a top 3 program. There is definitely a correct answer here. And the correct answer is that you should go to the program that is higher ranked and has a better placement record.
 
I will tell you right now. It is absolutely not worth it to go to a crappier program because of "fit" because
 
1) Better programs offer more opportunities
2) The goal is not to study under the faculty member that does exactly what you want to do. You want to be your own person. This means learning from other smart people who DO NOT do what you do. If you're trying to go to a program to work with one person and study just what they want to study, you're thinking about grad school and academia incorrectly.
3) And I can't emphasize this enough, there is about a 60% chance that you will end up specializing in and writing your dissertation about something that is different than what you think you want to do now. I came in as an IPE person and left as a methods person. 
 
So to put it bluntly, going to a lower ranked program because of something you think you want to do or someone you think you want to work with is a decision that you will most likely regret. Go to the best program, period.

Come again? I haven't deceived you. I was extremely clear in both the above and a follow-up post that I was not guaranteeing decisions would be released Tuesday, but that the department "expected to be allowed to release decisions on Tuesday." I further stated that this often takes a few days due to faculty travel or administrative hold-ups. Just because you haven't heard doesn't mean that other's haven't.
 
Reading carefully (and not lambasting those trying to help you) will serve you well in grad school, at Yale or otherwise. Then again, I should have known better than to post on here in the first place! It's "let no good deed go unpunished" territory this time of year!
 
Deuces and good luck to you all. 

This is precisely one of the major problems.  Many of those attempting to dissuade others from going to graduate school are implicitly comparing it against some ideal, instead of other viable career options.  Sure, there's plenty to complain about, but have they seen message board comments from failed lawyers?  Actually, pick any professional field, including medicine now, and you will find the same complaints.  Once I overheard a Professor downplaying the idea of getting a PhD, only to turn to another student to commend their decision to go to law school.  Seriously?  Check out lawschooltransparency.com to see how poor placement for JDs can be, and these are students who payed six-figures for their education.  Even an MBA doesn't guarantee high pay unless you're coming from a top program, but the higher up you go the more you pay for less return.  Ok, maybe that means it is best to just finish higher education after the BA level.  However, for some an extra five to seven years of study is a worthy deferral for having a job they like.  But life with only a BA isn't some paradise, either.  The median income for someone at that level is $46,900, which is slightly less than the salary for a new Assistant Professor at South Dakota State Technical College.  Fine, fine, the median income for BAs also includes everyone who got one in puppetry or politic . . . art history; they should have all gotten degrees in computer science.  Fair enough, but at that point you might as well tell them all to forego college because one can learn enough programming to get a solid job oneself while working on the side, and the relevant skills are all that employers care about anyway.  Problem solved: start shutting all the university doors tomorrow.  Really, those who are excessively doom and gloom about the situation in PhD programs* are saying "oh if only you knew what I knew" or "look at the burden I have to bear."  If this is coming from PhD students or Professors, why don't they simply leave academia and cut their losses?  News flash: no job is perfect, employment is never guaranteed, high pay is not an entitlement, you won't receive praise for simply doing your job, some people in every career will ultimately fail and many more will fall short of their top goals.  That's realism, the rest is mostly narcissism from people who think their lot in life should better for no good reason.

*Does not include the humanities.

So, I've been watching people talk about this issue for a while now, think this conversation is actually pretty productive, and I suppose I'd like to throw in my 2 cents. For whatever it's worth. Maybe nothing. Always nervous   .
 
I worked my way through undergrad in odd jobs, and since then I've spent a few years doing some freelance research work for policy folks in DC. Not that my background matters, just that I've talked to a lot of "career-level" people in different industries over the years. I think a dose of their perspective on what the working world is like could be important in a discussion like this. Especially because we're academics, trying to spend most of our lives cloistered away from it all on a university and even secondhand perspective is better than nothing. 
 
Whether they're a stage carpenter, grant accountant at a nonprofit, or even someone working at the Pentagon, not one of them spoke very glowingly of their industry. Especially people doing government work in DC. They talk about the restrictive job prospects, how pay is often going down, or how the environment can be so stifling that anyone proposing changes is trampled over, how frustrating rules and regulations are, how it's impossible to actually make a difference, etc. They say to be realistic, and please consider working in another field. Go to grad school or law school! And then of course, lawyers say the same thing about that. No jobs, incredibly competitive, too much debt, it's unrealistic to assume you'll succeed, etc.
 
I'm inclined to think it's a tired story people tell to vent. Or maybe everything does just suck? But then it's not THAT much better anywhere else either. If the world is going to smack me around for having dreams of a tenure track job, OK. The world can go ahead. Worse things happen to people than not getting their dream job. It's no reason to be a curmudgeon (looking at you, PSR). At least my job for five years will be doing something I love (research, school, TAing) before it's back to the grind.
 
And for the record, I'm probably just missing it, but I feel like I see a lot more lamenting a lack of realism lately than cases here of folks actually needing that dose of realism. Unless you count wanting to try in the first place, or being excited about acceptance to a #25-50 school as a lack of realism. In that case, humbug to you too, Mr. Scrooge. It's all a crap-shoot anyway.

This is precisely one of the major problems.  Many of those attempting to dissuade others from going to graduate school are implicitly comparing it against some ideal, instead of other viable career options.  Sure, there's plenty to complain about, but have they seen message board comments from failed lawyers?  Actually, pick any professional field, including medicine now, and you will find the same complaints.  Once I overheard a Professor downplaying the idea of getting a PhD, only to turn to another student to commend their decision to go to law school.  Seriously?  Check out lawschooltransparency.com to see how poor placement for JDs can be, and these are students who payed six-figures for their education.  Even an MBA doesn't guarantee high pay unless you're coming from a top program, but the higher up you go the more you pay for less return.  Ok, maybe that means it is best to just finish higher education after the BA level.  However, for some an extra five to seven years of study is a worthy deferral for having a job they like.  But life with only a BA isn't some paradise, either.  The median income for someone at that level is $46,900, which is slightly less than the salary for a new Assistant Professor at South Dakota State Technical College.  Fine, fine, the median income for BAs also includes everyone who got one in puppetry or politic . . . art history; they should have all gotten degrees in computer science.  Fair enough, but at that point you might as well tell them all to forego college because one can learn enough programming to get a solid job oneself while working on the side, and the relevant skills are all that employers care about anyway.  Problem solved: start shutting all the university doors tomorrow.  Really, those who are excessively doom and gloom about the situation in PhD programs* are saying "oh if only you knew what I knew" or "look at the burden I have to bear."  If this is coming from PhD students or Professors, why don't they simply leave academia and cut their losses?  News flash: no job is perfect, employment is never guaranteed, high pay is not an entitlement, you won't receive praise for simply doing your job, some people in every career will ultimately fail and many more will fall short of their top goals.  That's realism, the rest is mostly narcissism from people who think their lot in life should better for no good reason.

*Does not include the humanities.

This is precisely one of the major problems.  Many of those attempting to dissuade others from going to graduate school are implicitly comparing it against some ideal, instead of other viable career options.  Sure, there's plenty to complain about, but have they seen message board comments from failed lawyers?  Actually, pick any professional field, including medicine now, and you will find the same complaints.  Once I overheard a Professor downplaying the idea of getting a PhD, only to turn to another student to commend their decision to go to law school.  Seriously?  Check out lawschooltransparency.com to see how poor placement for JDs can be, and these are students who payed six-figures for their education.  Even an MBA doesn't guarantee high pay unless you're coming from a top program, but the higher up you go the more you pay for less return.  Ok, maybe that means it is best to just finish higher education after the BA level.  However, for some an extra five to seven years of study is a worthy deferral for having a job they like.  But life with only a BA isn't some paradise, either.  The median income for someone at that level is $46,900, which is slightly less than the salary for a new Assistant Professor at South Dakota State Technical College.  Fine, fine, the median income for BAs also includes everyone who got one in puppetry or politic . . . art history; they should have all gotten degrees in computer science.  Fair enough, but at that point you might as well tell them all to forego college because one can learn enough programming to get a solid job oneself while working on the side, and the relevant skills are all that employers care about anyway.  Problem solved: start shutting all the university doors tomorrow.  Really, those who are excessively doom and gloom about the situation in PhD programs* are saying "oh if only you knew what I knew" or "look at the burden I have to bear."  If this is coming from PhD students or Professors, why don't they simply leave academia and cut their losses?  News flash: no job is perfect, employment is never guaranteed, high pay is not an entitlement, you won't receive praise for simply doing your job, some people in every career will ultimately fail and many more will fall short of their top goals.  That's realism, the rest is mostly narcissism from people who think their lot in life should better for no good reason.

*Does not include the humanities.

This is precisely one of the major problems.  Many of those attempting to dissuade others from going to graduate school are implicitly comparing it against some ideal, instead of other viable career options.  Sure, there's plenty to complain about, but have they seen message board comments from failed lawyers?  Actually, pick any professional field, including medicine now, and you will find the same complaints.  Once I overheard a Professor downplaying the idea of getting a PhD, only to turn to another student to commend their decision to go to law school.  Seriously?  Check out lawschooltransparency.com to see how poor placement for JDs can be, and these are students who payed six-figures for their education.  Even an MBA doesn't guarantee high pay unless you're coming from a top program, but the higher up you go the more you pay for less return.  Ok, maybe that means it is best to just finish higher education after the BA level.  However, for some an extra five to seven years of study is a worthy deferral for having a job they like.  But life with only a BA isn't some paradise, either.  The median income for someone at that level is $46,900, which is slightly less than the salary for a new Assistant Professor at South Dakota State Technical College.  Fine, fine, the median income for BAs also includes everyone who got one in puppetry or politic . . . art history; they should have all gotten degrees in computer science.  Fair enough, but at that point you might as well tell them all to forego college because one can learn enough programming to get a solid job oneself while working on the side, and the relevant skills are all that employers care about anyway.  Problem solved: start shutting all the university doors tomorrow.  Really, those who are excessively doom and gloom about the situation in PhD programs* are saying "oh if only you knew what I knew" or "look at the burden I have to bear."  If this is coming from PhD students or Professors, why don't they simply leave academia and cut their losses?  News flash: no job is perfect, employment is never guaranteed, high pay is not an entitlement, you won't receive praise for simply doing your job, some people in every career will ultimately fail and many more will fall short of their top goals.  That's realism, the rest is mostly narcissism from people who think their lot in life should better for no good reason.

*Does not include the humanities.

This is precisely one of the major problems.  Many of those attempting to dissuade others from going to graduate school are implicitly comparing it against some ideal, instead of other viable career options.  Sure, there's plenty to complain about, but have they seen message board comments from failed lawyers?  Actually, pick any professional field, including medicine now, and you will find the same complaints.  Once I overheard a Professor downplaying the idea of getting a PhD, only to turn to another student to commend their decision to go to law school.  Seriously?  Check out lawschooltransparency.com to see how poor placement for JDs can be, and these are students who payed six-figures for their education.  Even an MBA doesn't guarantee high pay unless you're coming from a top program, but the higher up you go the more you pay for less return.  Ok, maybe that means it is best to just finish higher education after the BA level.  However, for some an extra five to seven years of study is a worthy deferral for having a job they like.  But life with only a BA isn't some paradise, either.  The median income for someone at that level is $46,900, which is slightly less than the salary for a new Assistant Professor at South Dakota State Technical College.  Fine, fine, the median income for BAs also includes everyone who got one in puppetry or politic . . . art history; they should have all gotten degrees in computer science.  Fair enough, but at that point you might as well tell them all to forego college because one can learn enough programming to get a solid job oneself while working on the side, and the relevant skills are all that employers care about anyway.  Problem solved: start shutting all the university doors tomorrow.  Really, those who are excessively doom and gloom about the situation in PhD programs* are saying "oh if only you knew what I knew" or "look at the burden I have to bear."  If this is coming from PhD students or Professors, why don't they simply leave academia and cut their losses?  News flash: no job is perfect, employment is never guaranteed, high pay is not an entitlement, you won't receive praise for simply doing your job, some people in every career will ultimately fail and many more will fall short of their top goals.  That's realism, the rest is mostly narcissism from people who think their lot in life should better for no good reason.

*Does not include the humanities.

Based on your experience, I would say that pursuing a PhD in political science with a focus on China is the best option.  I don't think a PhD in Chinese Studies would make you competitive for academic positions and wouldn't be much of a leg up in the type of work you are already doing, whereas a PhD in political science would be a benefit for both.  I would look at any departments that have a strong comparative focus on China and with some really prominent China scholars.  Harvard, Yale, Stanford, and Columbia are good.  Berkeley has O'Brien and Dittmer, and is probably the best option; MIT has Fravel; GWU has Shambaugh; Cornell has Mertha and Carlson; Michigan has several China scholars; UW Madison also might not be a bad choice, since Manion is still there.  Any of those would be a great place to get a PhD in political science with a focus on China, and because you have experience they would probably fund your language training.

I'm in at Irvine.  First admittance, so...there's one.

Even if that's all undeniably true, PhDs seem to do just fine in non-academic research positions.  I've worked in several such environments, and PhDs were more desirable for research positions than MAs, MPAs, and at least as desirable as JDs (who paid significant money for their degrees).  Searching the public salaries of my state, workers with PhDs are paid handsomely.  Maybe these employers, and others like think tanks and private firms, have been unaware that PhDs are ill-prepared for research outside academia and need you to explain to them how they could significantly cut costs by hiring other candidates.

Even if that's all undeniably true, PhDs seem to do just fine in non-academic research positions.  I've worked in several such environments, and PhDs were more desirable for research positions than MAs, MPAs, and at least as desirable as JDs (who paid significant money for their degrees).  Searching the public salaries of my state, workers with PhDs are paid handsomely.  Maybe these employers, and others like think tanks and private firms, have been unaware that PhDs are ill-prepared for research outside academia and need you to explain to them how they could significantly cut costs by hiring other candidates.