A family member of mine is going through a similar situation so I'll break it down for you the same way I did for him. There are a few important factors to consider other than cost and prestige (but we'll talk about them anyway).
1) Cost is obviously a factor, like most people have said above, go to the cheapest one possible. Not just because it limits your future debt, but it also put less stress on you in terms of deciding residency (if you're strapped to 400K in med school loans, going to a residency in a city with high cost of living is going to be a tough sell), early financial independence (you can't start investing early as a young attending if you still got a rolling snowball of student loans on your back), and lifestyle/relationships (your vacations/weddings/honeymoons are gonna be more meager than you want)
2) Prestige, how important is it actually? Every extra level of training you do, the less the previous level matters. This sounds kind of harsh but its true. Once you start med school, no one cares where you went for college. Likewise, once you start residency, no one cares where you went to med school. On the other hand, where you do residency is actually important. But graduating from a big name med school won't really help you get into a big name residency program (see below).
3) Competitiveness: I've seen middle tier university program students into in top 3 residency programs and I've seen top 10 med school students not match at all. It's not so much about where you came from as it is how competitive YOU are. If you absolutely destroy the USMLE exams, top of your class, and get AOA/Gold Humanism, no program is gonna turn you down. The prestige may come into play if you and one other applicant is competing for the last spot on a program's list and you guys both have the exact same credentials, but he went to Harvard med and you went to State U.
4) This ties in to the last point and it is really important. Do you want to be a big fish in a small pond of a small fish in a big pond? There are going to be smart people in every class at every school. There was a guy in my class who could memorize every word of every 800+ slides for every test (not exaggerating, we tested him, he could tell you word for word what was on line 5 of slide 8 of pptx #7) and I went to a middle tier state school. If you go to a big name school, the level of competition [I imagine] will be even higher, making your chances of graduating top of the class/getting AOA even tougher. Of course, some people thrive on competition, so how important this actually is is for you to decide.
5) Research: this might be one of the most important things if you want to do GI. There are research opportunities everywhere, not just at big name places. If you can get some done as a medical student, it will definitely give you a leg up because residency is BUSY. Easiest way to find out how much research opportunities there are is to look up the GI faculty at that hospital, then look up their most recent publications in pubmed/google scholar. If they are continually cranking stuff out/securing grants, that's a good sign. If their last publication is back in 1987, they're probably not as active on the research front. Chances are most of their research is too advanced for you, but the more faculty doing active research, the more likely you are to find a project suitable for a med student.
6) Ignore how awesome the GI fellowship is at the med school you are applying for. You are at least 6 years away from applying and I would say most people don't do med school, residency, GI fellowship at the same institution. Plus the awesomeness of a fellowship program can change so dramatically in just a few years. Imagine a faculty of 20, in 6 years maybe 2 retires, the program director changes, 3 get new jobs elsewhere, 3 decide to up their research time, another decides they only want to do clinical duties without any teaching, 2 more goes part-time. Thats a whole different program now! Not saying that happens everywhere or all the time but it would be silly to plan your life based on something that can change so easily.
7) Support: med school is hard. It is a completely different beast from college and the adjustments in those first 6 months are rough. I always tell my students if you have the opportunity to do med school closer to home or locations with good support outside of the classroom, do it. I am not sure if you are from the state of one of those schools and everyone is different, so that is another thing you have to decide for yourself.
Hope that helps!
