I know most people feel like prestige is a huge factor, and perhaps it is. We can't really know as first years or as premeds how important prestige really is, but I would say that you learn the same material essentially where-ever you go. Therefore, choose whichever place would make you the happiest. How happy you are will definitely determine your success in med. school. I didn't even apply to most schools in the NE (including places like Harvard, UPenn, Yale, etc), because I knew for a fact that I wanted to be in CA. And even though I knew it'd be hard to get in to a UC school as an OOS student, I still tried really hard, because I knew I'd be happy in CA. And I was right. I am super happy here.
I can't speak for Harvard, but UCSD has amazing resources. We are probably the only school in the nation that has an Office of Educational Support Services, which houses 4 amazing professional tutors. They hold PhDs and masters already, and act as professional students that take our classes with us and then lead review sessions (both in large group and small), create practice exams, study aids and help with USMLE Step 1 in second year. Some of them have been there for over 20 years and know the material front and back and are a huge resource.
Besides this, the support network is great at UCSD. Besides the big-sib little sib program, we also have faculty mentors specifically assigned to us and the administration is extremely receptive to student input.
And if you care about grades, well, we are pass/fail now. In addition, a fourth year told me that his year, the class average step 1 was supposedly something like 235, with a quarter of the class scoring above a 245. As a reference in case you don't know what Step 1 scores are like, the national average tends to be around 220. The average for Derm (perhaps the most competitive specialty there is) is 240. We had 3 4th years match into Derm this year and plenty into other competitive specialities like radiology, anesthesiology, ortho, etc... We have also always been well trained during third year to prepare us for residency.
Plus, the free-clinic system here is a great way to learn and get the continuity in patient care that you won't be able to get elsewhere. Being a part of the specialty clinics gives you a glimpse into the field at a much earlier stage than waiting around for 3rd year rotations.