The only really good way to be able to compare the two schools is to interview at both. Yes, Stanford has a program of specialization, while Harvard doesn't (compulsory "med school major" vs. more unstructured time). Harvard focuses very strongly on PBL, while Stanford has more lectures. My personal preference is Harvard. Really, though, I think that it's very hard to judge until you've actually visited the schools.
On an unrelated note (please humor me)... For some bizarre reason, everyone in my family is pressuring me towards Stanford... I haven't even been invited to interview there, but everytime I call a family member, I hear "What about Stanford?", "Sure, you say that <School X> is your top choice, but WHEN YOU VISIT STANFORD YOU'LL CHANGE YOUR MIND!!!", and "I think Stanford's a great fit for you." Seriously, EVERY TIME I mention medical school, they shove Stanford in my face. I called to tell my dad that I had been accepted to the University of Rochester (my first acceptance). His response was "Oh. Uh huh. Have you heard anything from Stanford?"
Yes, my dad went there for his Master's degree in Economics and I lived in Palo Alto for a year (I was in first grade). Yes, my first memory of being in a medical situation was at a Stanford hospital (my dad was going in to have his parathyroids removed and I remember pleading with my mom to be let into the O.R. because I really wanted to observe the surgery- I know, it's cornier and cheesier than a giant bag of Doritos). I am seriously VERY CLOSE to withdrawing from Stanford because I'm so sick of hearing their name. Yes, Stanford is an awesome school. I used to love Stanford. Now that all of my relatives are on a crusade to entice me to go to California, I'm far, far less enthusiastic. Alright, end of rant. So, one advantage Harvard has over Stanford is that my family isn't going freaking BANANAS over Harvard.