One major difference between the schools is housing. At Harvard, housing is guaranteed for all 4 years, while at UPenn: http://cms.business-services.upenn.edu/residential-services/housing-options/housing-options.html
As such, the majority of undergraduates in their junior and senior years live off campus at UPenn. That could be a plus factor for some students, while a negative for others. IMHO, it’s a negative, as Harvard’s residential housing system is far superior to any of your choices at UPenn.