psstein

The job market comments was more based on my own understanding of the situation. The AHA has claimed that roughly 55% of all history grads end up with some full-time academic position, but they're very vague as to what that means (TT, Full Time non-TT, Adjunct, Postdoc, etc.). Brian Leiter's blog tends to be pretty good about issues with philosophy placement. Here's a recent enough (Oct. 2018) article: https://leiterreports.typepad.com/blog/2017/10/placement-in-phd-granting-program.html
As for the MA, I'm glad we agree about the Chicago programs! I tend not to hold them in the highest regard, as I've seen woefully underprepared students come out of them.

My partner is in history, at a non-fancy but R1 university with a pretty strong faculty, and her advisors have a policy of strongly discouraging anyone from seeking academic employment in history unless they are studying Asia or Africa. So it certainly isn't good.
Whether philosophy is any better, I'm not sure. But the thing is, you have to consider not only the philosophy market, but the sub-market for history of philosophy, Medieval specifically. And that's also a very very bad market, at least from all the data that has been made available by the APA and all the philosophy bloggers and so on. The less in-demand (or the more over-represented) your sub-field is, the harder it is to get a job.

Don't go to the MAPH/MAPSS programs; they're a colossal waste of money. Take some upper-level or grad courses at your current institution (since you work there). This will help you get letters, possibly give you a starting point for a writing sample, and give you some exposure to the discipline. Then apply to programs, with plenty of fully-funded MA programs on your list.

It was the hardest decision I've ever made but I have declined Penn's offer and will be heading to Yale next year. 
I honestly still feel very conflicted, but I am incredibly excited for what is to come. 
Best of luck to everyone else! 

More significant than you'd probably hope. He sounds like a great guy and a good advisor. There are two very significant concerns here:
1. Will you be able to get the type of support you need from an absentee advisor? Are there other faculty you can lean on at Penn? Just anecdotally, a friend finished his PhD last May. His advisor had recently retired and was in the middle of doing other things. He said that it was impossible to get in contact with the guy-- it took weeks to get comments on drafts and feedback. Nothing to do with ability, but a lot to do with availability.
2. Do you need a JD? Graduate programs already take an inordinate amount of time (6 years is a floor at most universities). A JD/PhD will only extend that period. I also want to say that a JD is, in a very real sense, a far more useful degree than a PhD. The job market for law is bad. The job market and long-term outlook for academic history is nothing short of miserable.
This is nothing short of an absolutely giant red flag. A lack of a proven track record of success, combined with a nonchalant attitude to the job market should set off a very loud warning klaxon. The market is brutal, even for someone from a top-tier Ivy. As I've said many, many times, the point is not to get into graduate school. It's to find a job after graduate school.

It feels completely surreal to say this, but I have accepted an offer from Northwestern. On my way home in the wee hours of Sunday morning, I said out loud to my partner, "I have fully accepted that in two days I'll get an email from them telling me that there's no space for me this year." Two minutes later, the offer email came in (at 2 AM Chicago time--deadlines don't respect normal sleep schedules). 
Even after everything I've put into this process, I still spent the day yesterday in deep reflection on whether I really, truly want to take this leap. I wanted to be sure that I was accepting their offer because it's the right one, not because it's the only one. Ultimately, this was the best option all along to support the work I want to do.
Best of luck to everyone who's making a decision today, or waiting on one. I still can't quite believe it, but it's real. 

More significant than you'd probably hope. He sounds like a great guy and a good advisor. There are two very significant concerns here:
1. Will you be able to get the type of support you need from an absentee advisor? Are there other faculty you can lean on at Penn? Just anecdotally, a friend finished his PhD last May. His advisor had recently retired and was in the middle of doing other things. He said that it was impossible to get in contact with the guy-- it took weeks to get comments on drafts and feedback. Nothing to do with ability, but a lot to do with availability.
2. Do you need a JD? Graduate programs already take an inordinate amount of time (6 years is a floor at most universities). A JD/PhD will only extend that period. I also want to say that a JD is, in a very real sense, a far more useful degree than a PhD. The job market for law is bad. The job market and long-term outlook for academic history is nothing short of miserable.
This is nothing short of an absolutely giant red flag. A lack of a proven track record of success, combined with a nonchalant attitude to the job market should set off a very loud warning klaxon. The market is brutal, even for someone from a top-tier Ivy. As I've said many, many times, the point is not to get into graduate school. It's to find a job after graduate school.

I would find this very, very off-putting--I was in a similar position w Penn a few years ago. My prospective advisor seemed amazing but she was also very near retirement and I couldn't imagine who would become my primary advisor if she were suddenly unable to advise me. I would highly stress the importance of a supportive team over a supportive individual (and I wouldn't put too much emphasis on big names, though this person also sounds like they have a record as a good advisor, so that's a bit different). To me, a stranger reading your post, it sounds like you'd be more secure at Yale, and feeling secure in your program is really important. 

If you've not done so already, do what you can to schedule "exit interviews" with those at your current institution who have helped you get to this point. Pick their brains for suggestions on how you can improve as a historian at Villanova.
Please consider the advantages of not, repeat, not asking what you could do to become a stronger applicant.

The US News and World Report's rankings are worthless. You should go to School A. Your advisor's reputation will follow you long after s/he dies. Think about Prof. B's time constraints. Running academic institutes is time consuming. My advisor is on multiple committees and it can be a chore to meet with her at all.
You should also look at placement. Having a "star" advisor is worthless if s/he can't place students.

The US News and World Report's rankings are worthless. You should go to School A. Your advisor's reputation will follow you long after s/he dies. Think about Prof. B's time constraints. Running academic institutes is time consuming. My advisor is on multiple committees and it can be a chore to meet with her at all.
You should also look at placement. Having a "star" advisor is worthless if s/he can't place students.

Unless either of these institutions is truly renowned in your field (e.g., MSU for African history or Georgetown for Mideast history, which are really rare examples), look at your prospective advisors' placement records. If neither have placed many students, compare funding and research resources.

I would encourage you to refine specifically why you want and need the languages you're taking up. I understand @telkanuru's point about German, but I'm not sure I agree with him. Certainly some sub-fields benefit very much from having access to German language sources, including my own (history of medicine). With other sub-fields, however, focusing intensely upon French and Latin will prove far more useful. German history of science literature, for example, heavily focuses on late 19th/early 20th century physics and the development of disciplines like physiology, biology, and organic chemistry.
I do echo his call, however, about finding a very specific time period and framework. For example, my MA project is about attempts to control syphilis, focusing on human medical experimentation, in both the US South and one Latin American country between 1945 and 1965. My SoP discussed French Jesuits in the New World and their role as knowledge producers and circulators. My question for you is, precisely: what do you want to do and why do you want to do it? You don't need to have a completely articulated, entirely set out framework, but it does help to understand precisely what you want to look at and why it matters. I would suggest that even your current interests are far too broad. Obviously, some of the work of the MA (and PhD) is about refining and narrowing your interests, but as you show below, you have a lot of interests. I'd strongly recommend choosing one and really digging into it. Maybe it's my own work showing, but the intersection of religion and public health sounds fascinating. I can think of many profitable ways you can go with that topic alone (e.g. church attendance as a form of medical surveillance in 15th C. Vienna), but the overarching point is that you need to become more of a specialist, rather than someone with diffuse interests.
By the way, having diffuse interests is not bad, but you need to focus very heavily on one, without seemingly overly narrow. You should have a significant amount of intellectual curiosity, but you should also read with what one of my professors calls "active plunder," how a book allows you to do what you want to do.
 

I would encourage you to refine specifically why you want and need the languages you're taking up. I understand @telkanuru's point about German, but I'm not sure I agree with him. Certainly some sub-fields benefit very much from having access to German language sources, including my own (history of medicine). With other sub-fields, however, focusing intensely upon French and Latin will prove far more useful. German history of science literature, for example, heavily focuses on late 19th/early 20th century physics and the development of disciplines like physiology, biology, and organic chemistry.
I do echo his call, however, about finding a very specific time period and framework. For example, my MA project is about attempts to control syphilis, focusing on human medical experimentation, in both the US South and one Latin American country between 1945 and 1965. My SoP discussed French Jesuits in the New World and their role as knowledge producers and circulators. My question for you is, precisely: what do you want to do and why do you want to do it? You don't need to have a completely articulated, entirely set out framework, but it does help to understand precisely what you want to look at and why it matters. I would suggest that even your current interests are far too broad. Obviously, some of the work of the MA (and PhD) is about refining and narrowing your interests, but as you show below, you have a lot of interests. I'd strongly recommend choosing one and really digging into it. Maybe it's my own work showing, but the intersection of religion and public health sounds fascinating. I can think of many profitable ways you can go with that topic alone (e.g. church attendance as a form of medical surveillance in 15th C. Vienna), but the overarching point is that you need to become more of a specialist, rather than someone with diffuse interests.
By the way, having diffuse interests is not bad, but you need to focus very heavily on one, without seemingly overly narrow. You should have a significant amount of intellectual curiosity, but you should also read with what one of my professors calls "active plunder," how a book allows you to do what you want to do.
 

Really, have you considered taking the next year off to narrow your interests a bit and self-study a language? As you know from learning Italian, learning new languages takes dedication. And it is very challenging to do so when you're loaded with graduate-level coursework.  There is a reason why most PhD students try to make sure that their main research languages are at intermediate/advanced stages when applying, or take intensive summer courses (which will then eat up time used for studying comprehensive exams and research). My $0.02.

As everyone, from your professors to the adcoms to the posters on this board, has been telling you over and over again, you don't need flexibility. You need focus. If you were actually ready for this next step, you wouldn't be asking us which languages to take. You would know.
An MA on the way to a PhD is a time to refine your area of study, not discover it. You have extremely limited time and need to hit the ground running; many of the people you will be competing against started their language training in middle school. At the very least, at this point you need to be able to articulate a time period, a geographic region, and a structural approach (e.g. I want to study the south of France during the central middle ages through the lens of postcolonial theory). How else are you supposed to pick what to take?
You come across as interested in the idea of having a PhD rather than any particular subject of study. Nothing you've said instills confidence that you've even begun to plan to fix this. Unless you do, your next application cycle will go no better than your last. I would strongly suggest you take @TMP's advice, look into your deferral options, and spend some time meditating on your own motivations and desires..

Yes, definitely learn French and Latin. I will also say though that you should take other language courses you’re generally interested into because sometimes those languages can come in handy for the future. For example, learning Arabic may sound out of left field, but if you’re interested in it and eventually learn some Arabic, you may even be able to utilize it somehow in your research, or at the very least, have an extra skill that could make you more marketable.

If you want to study Medieval I would prioritize Latin, then German, then French. Latin is definitely the most important, so you should being right away. Learning Latin first will also help you immensely with German, because it sounds like you have not studied a case language before. If you are already strong in Italian I would not worry so much about French - I imagine you can probably already make a go of it just using your Italian. Probably a semester of French for Reading is all you will need. 
Not to be harsh, but unless you are committed to devoting 2-3 years of INTENSIVE study to Russian it is probably too late (and not worth it) to get involved with a Russian topic. 

Would you say in that order, too? 
Latin and French are non-negotiable, IMO. You can get around not knowing German in certain sub-fields. 

Would you say in that order, too? 
Latin and French are non-negotiable, IMO. You can get around not knowing German in certain sub-fields. 

In that case, Latin, French, and German if you want consideration from any decent program.

It depends on what you want to do. If you want to do Medieval/Early Modern, Latin is the language of most official documents/manuscripts/etc. 
It's probably not bad to know French, just so you can have some access to secondary literature. I'm obviously showing my history of science bias, but some of the foundational literature is in French. You probably don't need Old Church Slavonic unless you're planning to work on something involving the Orthodox Church.
Importantly, though, determine if you want to do Medieval, Early Modern, or modern European history. You're not always going to be wedded to one over another (18th century sort of falls in between), but you should choose one to focus on.

I'd stay in the program. Once you are in the dissertation stage, you are much, much more free to explore your own interests and meet others who share the same questions.  This can be done by going to conferences, reading conference programs and journal articles, and reaching out to scholars in your vicinity of your archival research.  It is expect that you expand your knowledge and network beyond what you've been exposed to during your coursework years. 
There are plenty of professors supervising dissertations outside of their own inquiries because students change directions and that's perfectly normal.  A good adviser will be honest with you and say, "I'm sorry, I can't supervise this kind of dissertation."  It sounds like your adviser is still confident and wants to keep guiding you.  Have faith.
Even if you try to transfer at this late stage, you'd still be looking at 2 years of coursework elsewhere and then another year of comps studying.  That's not a good way to do the PhD unless ALL of your advisers have left the program, which it sounds like everyone on your "committee" has stayed. They may not be interested but you can find mentors elsewhere, even within early modern Europe.  Are there other historians sharing similar questions?  To be competitive on the job market, you need to be able to interact across geographical and temporal fields. 
I know it's lonely to be the only one in your program in your own field (same!) but that's why you need to make an effort to get yourself out there and make connections with graduate students and professors in other schools.  I've been doing that and am finding amazing support from them than I would have if I wasn't proactive.

It's not just $2000 when you compare cost of living in New Haven vs. Cambridge! But I had been told the Harvard package was up to $35,000... strange.
If you do ask, just be diplomatic. You have some concerns about living in such an expensive real estate market and Yale's offer would seem to create less stress on a personal level, and is there any way for Harvard to assist with this?

You shouldn't bring this up with anyone outside of the people in a position to do something about it. I would also recommend sending an email saying something along the lines of "I want to attend Harvard for reasons x/y/z, but I currently have a slightly better offer from Yale, etc. Would it be at all possible for the department to increase my level of stipend?" Or something like that at least. You want to be as polite as possible about it, because money can always get touchy, even at places richer than God Himself.