I've been mulling over whether to answer this question, because I don't know much about Tufts or AE. I don't think you can really go wrong with any of these schools, but I know if it were me, I would choose Rochester. To me, the only thing Tufts/AE have over Rochester are their locations (I'm a huge fan of Boston). Otherwise, to me, there's no real competition. From my understanding, Rochester is more highly regarded than Tufts (although, I have heard Tufts does well with residency placements) and is less expensive; AE and Rochester have pretty similar reputations and costs, but to me Rochester's program (curriculum, humanities electives, international opportunities) can't be beat. You throw that on top of the fact that everything's basically brand new (including the PBL rooms, which I think are pretty cool) and the fact that it's connected to the undergrad campus (which I think is beneficial for a med school) and you have a lot going in favor for it.
All that said, I made my choice (Rochester) based on a gut feeling I had after my interview. I suppose I was lucky in that sense, because I just didn't have that feeling at the other places I interviewed. There was just something telling me that I could really see myself there if I was accepted and I'd be the happiest there (by far) of any of the schools I applied to.
Whatever you decide, I'm sure you'll be happy. They're all great schools.
Good luck.