I pretty much agree with everything Supercluster already said - if you have one academic blip they won't throw the rule book at you. The faculty really does try to help you out (of course, you have to show them you're not just slacking off). I was on a couple waitlists last year but I'm actually pretty glad that I ended up here, it's turned out to be a good fit for me.
I really think that for the most part, a "School A vs School B" decision comes down to personal factors. Don't let board scores or perceived academic "superiority" make your decision for you. Think about what type of city you want to live in - a lot of people here complain about Buffalo not being NYC but deep down inside they don't mind that much. But then I do know one or two people who really don't feel at home here - this is just the wrong kind of city for them in particular. Similarly, if I were in NYC (for instance) I don't think I'd be quite as happy - that's not the right kind of city for
me. Also think about whether you want to be close to your family and friends - that can make a big difference in terms of being able to find support for when you're having a tough time.
Besides those non-academic things, think about how you learn best - do you find lectures generally helpful for your learning? Most schools have a contigent that swears by independent learning and who never go to lecture - Buffalo's no different. If you can't stand lecture and go to a school with mandatory attendance (I don't think Downstate does, I'm just saying as an example) then that's probably not a good fit for you.
Both Buffalo and Downstate have probably pretty similar board performances from year to year and similar caliber match-lists. Don't base your decision on the fact (? this thread is the first I heard of this) that Buffalo's average last year was 5 points higher than Downstate or that Downstate had X matches in X specialty, including a high prestige match at X school's residency program. If you do well at either school, you'll match where you want to match in what you want to match. It's easier to do well when you're at a school you love in an environment that enhances your ability to learn and perform.
I really did (for the most part) enjoy my first year at Buffalo. Some of my friends enjoyed it as much as I did, some of them had a mixed experience, and some are just relieved it's over and they're out of Buffalo for the summer. Everyone's going to have a different experience at all the different schools, so just do what you can to find the school with the environment that matches you best, not just the school with the highest board score and the "best" residency matches.
I think I'm repeating myself at this point so I'll stop. Good luck with your decision(s) and with your first year. And enjoy the summer
.