Well, like I said in my original post, I think that bjorntsui is right with respect to the "it is what you make it" sort of premise. But it's also very important to take into consideration the fact that the programs in quant/econ are probably more different than s/he let on. I apologize if it just seems like I'm rehashing what I said earlier, but both points are key with regards to what we're talking about.
Here's one example of what I mean at a more macro level:
MSFS has quant/econ coursework, but if you look at their concentrations and illustrative curriculum, you'll see that some of the courses that qualify for the degree are offered from other departments of GU. This fact could be both an advantage and a drawback, since I would think you would have broader access to courses across different GU programs, yet at some point you probably lose the international relations/affairs focus and start getting into other fields/disciplines/areas of study.
SAIS seems to be the opposite; what you see is what you get. The benefit is that the program is specific and unified, which could make for a more cohesive experience (in this area) than MSFS. The disadvantage, however, could be that if you're interested in something and they don't offer a course on it, you're pretty much out of luck, relatively speaking.
At the end of the day (or should I say program), however, prospective employers are going to want people that know their stuff, which is where bjorntsui's statement rings true. If you worked hard to get the knowledge and skills necessary for specific types of jobs, and you have what recruiters/interviewers want, I'm not sure that the school will matter that much. Where the school will make the difference, I would think, is if you know that a school can better prepare you in a specific area of quant/econ than the other. In order to find that out, you'd have to do some extra research about course offerings, the professors who teach the courses, etc. It might take some digging, time, and effort to do so, but trust me, it'll be well worth it, especially if you know what you want to do. You don't want to choose a school and then somewhere down the road realize that maybe another school would've been better for developing an area that you wanted to work in.
The reputation factor could have some merit, but I think it exists more along the lines of the initial part of applying for jobs. As in, a screener went to school X, or works with someone who went to school X, and depending on that person and their abilities, may have a favorable view of that school. They might see your application and see you went to school X, and this fact coupled with your coursework and experience, may lead to an interview. At the end of the day, though, the decision is going to depend on, again, what you bring to that organization, and not just in terms of the knowledge and skills, but other factors such as your personality, ability to work in a team, or anything else the job would value that's totally unrelated to what we're talking about.
I apologize for the post being so long, but there's something else that might be helpful to think about: competition in this quant/econ area. When you start looking for jobs, you're essentially competing with not only those at your school (and not just your graduating class), but also with candidates from all the other schools. I cannot stress this enough, but you HAVE to assume that there *will* be people, for instance, that went to X school to focus solely on Y and took all the classes possible in that area. So after researching whatever schools you're looking at, try putting yourself in the position of, "I went to Z school and took all that I could on Y...how would I compare with someone who went to X school and took all of that school's courses on X (and did well in them)?" In other words, try imagining the worse-case scenario (to you) of your competition at the other school and their preparation, and then given your prospective preparation asking yourself, "Will I be competitive?" There will most likely be lots of similar competitors, so keep this in mind, as well as a rough idea of the job market for the kind of position you want.
To help with this sort of research, you could also look for past and present job openings in either your specific focus or this quan/econ area in general, see what those types of positions look for in a candidate, and see which schools could better prepare students for those jobs based on your school research.
Finally (I know I know), this specific advice could change depending on your situation. I assumed, maybe wrongly, that you're thinking about focus W among X and Y schools. Now if you're contemplating focus W at school X vs. focus Y at school Z, I would at the very least frame this advice differently. But anyway, I hope this perspective helps, and if I only wrote things that everyone already knows, I apologize!
