That's a toss up (and it'll depend on who you are). I will say this...after visiting Stanford, almost every other medical school program in the nation seems like it has some catching up to do. They are resource overloaded (there's so much money available and people wanting you to use it) and one of the few schools that really actively supports interdisciplinary supports to a real meaningful degree. How 'bout a BioDesign course that combines law students, med students, business students, and grad students for making new innovative biomed solutions that often emerge as real products from the class? I was impressed by the Stanford med students more so than students I met at any other school.
Having said that, Philly is so infinitely >>>>>> Palo Alto for me that I'd take Penn over Stanford personally. It's hard to argue that Penn's curriculum isn't awesome as well. I think Stanford might have a slightly superior program because of all the monetary support and real, seamless access to it's research and grad school community (Stanford Law and Business), but the feel and culture of Penn and Philly mold better with me.
I'm keeping my name on at both places and actively pursuing them, but in a dream world of getting in off of both, I'd chose Penn.