Cognitive dissonance is a funny thing. We always justify our decisions based on the present because we can't possibly evaluate what would have happened elsewhere. It's better not to think you would have been better off somewhere else because that kind of thinking would just hurt yourself.
I was interested in neurosurgical topics when I was applying, something that both Baylor and NU seemed kinda shrug in (Baylor probably somewhat better). My interests changed towards Radiology for a couple reasons. The research I do now I couldn't be done at Northwestern OR Baylor and had I gone to one of these schools I more than likely wouldn't have done a Radiology PhD. Who knows what would have happened. Would I have made the best of things where I was? I like to think so considering my personal life here has been very rocky and I'm still managing to do pretty well.
Still, the value of the big name PhD is something we've debated before and will continue to disagree on. I go to a big name school, but my PhD is in a small lab with a PI who is only known in a small area of our field. Still, when I go to apply for Radiology and do research later I will be one of the few who did their PhDs in Radiology. As far as I can tell, this is a major advantage, far outweighing having done a PhD in a lab that is big name in some other area of medicine. I've also seen so many students in big name labs have major issues that I can't at all recommend being in a big name lab just because it's big name.
I also don't think that anyone is going to split hairs on the name of your MD/PhD program as long as it is in the top-25.
Anyways, it must be stated that this is just my personal bias. For me location and personal life issues are more important than things like prestige and they always have been. When I go off to residency it's entirely possible I will pick on location again and I have no issues with doing that. I was fortunate that I got my choice of location and program when I applied, but I still would have chosen location if I had to choose again. Given that I ended up with both prestige and location, I still think location is the right decision. But, that's just my opinion.