You don't have to KNOW what would help you do best, but didn't you even think about it? If we're comparing a small school with PBL in Cleveland (Lerner) to a large school with lectures in California, it would come down to a coin flip for you?
I think the most important factors are, in approximate order - location, cost, "feel" that you got from a campus visit and interview, M3/M4 rotation scheduling, general teaching style, and that's about it. When I made my final choice between two schools, it was because I liked the feel of one more than the other, as well as the fact that the "other" had something like 16 weeks of required away rotations as an M3. No thanks.
Well, I'm not really the best example since I plan to do translational research and stay in academia. And academia is overly snobby, so 'name' does matter when you're applying for grants as a junior PI and stuff (many, many sources on this so no need for argument even if I'm wrong).
But if my main focus was to be a physician, it really would not be clear:
Lecture vs. PBL: I've had lectures all my life and always done well in them and learned relatively efficiently through them. I also enjoy solving problems, so PBL sounds great. But I've never experienced PBL in any sort of depth.
Large vs. small: No idea, my high school was medium-sized and my college was large. All medical school classes are relatively small.
Location: I've lived in Oregon/California all my life and quite like it on the West Coast. That said, I would also enjoy a stint on the East Coast. Also I moved around 7 times as a kid in both small towns and large cities. Liked both, each has its unique advantages.
Cost: California schools sure are nice, assuming I get in, but you only go to medical school once and you have the rest of your life to save up money. I did not need loans for undergraduate (scholarships, work, parents) so my finances are reasonable either way.
M3/M4 rotation scheduling: Being able to do some electives M3 is definitely a plus, but it is very rare for schools to offer that. Some away rotation opportunities are nice, but it is very common for schools to offer that. 16 weeks of mandatory away requirements as an M3 is not something that any schools I'm applying to has; I've never even heard of that before!
P/F vs H/P/F: I would prefer P/F because I want to be more relaxed, but I also know that I tend to do well in competitive environments. Importantly, I know that I tend to do well in competitive environments even when I'm at the bottom. OTOH, I'm getting too old for this.
Feel during interviews: All the students seemed happy at all the schools I've been to. Interviewers seemed very nice. I have to say there is one school that stands out a bit (positively), but then other people said the students there were miserable; I'm not sure how much I should trust 4-5 hours of observation (2 hours of which are in the room waiting for interviews or interviewing) and one student host (who may or may not be representative). There's no school that struck me really badly.
I don't know if I'm an exception here? I'm really, really 33/33/33 about the schools I've been to so far--and not in a bad, way: I've been consistently impressed.