I'm an MS4, and I've actually been thinking about this a lot - whether I chose my med school wisely.
A few things that I thought were important when applying did turn out to be important, while others turned out to be completely unimportant. One of my considerations was location, and I've found that this was a very smart move. I like big cities, especially New York, and I am incredibly glad that I chose to come to this city. Another smart move was choosing a school that gave you a lot of free time during the first two years - time to enjoy NYC.
I also chose partly based on prestige of the school, and that turned out to be a good decision also. Despite what some people on this board will tell you, your med school DOES matter when you are applying to residency, and I'm glad that I go to a pretty good school.
Now for the things that weren't important: the "early clinical experience" that schools like to brag about. Shadowing a doctor during your first and second years of med school for one day a week may seem cool - BUT IT'S NOT! At least not in my experience. In med school, you have to learn a ton of information in a short amount of time. The amount that you learn through this shadowing is not worth the amount of time that it eats up.
As for choosing based on curriculum: it's hard to know what will work for you. I tried PBL and hated it. From talking with my classmates, the majority thought that PBL was pretty useless, although there is one girl who loved it. As for systems vs. subject based, you probably don't know which will work for you.
My final decision on where to go to med school was based on "gut feeling" - whether I liked the people I met on interview day, basically. I can say now that this is a poor way of choosing a med school. The people you happen to meet are not likely to be the people you will actually spend the most time with (you are not going to be hanging out with the great med students you meet, as you will more likely be hanging out with students from your year, and the faculty members who interview you may never see you again).
In the end, you just have to make a decision, and you may not know until years later whether it was the right one. I think I made a pretty good decision, but perhaps not the best one (I wouldn't choose PBL and I would prefer not to have that ridiculous early clinical experience).