One of the most popular squares in Philly is Rittenhouse Square.  In my opinion its the best for photos and the bonus with Rittenhouse is that there aren't any permits required to shoot here.  Its a great spot to do the majority of your wedding party formals to get some greenery in the background as well as some picturesque settings to work with as well with the fountains, gardens, and surrounding buildings.  All within a couple blocks of a lot of hotels and venues in the downtown area and only a handful of blocks away from the South Broad/City Hall spot too if you want to hit both spots quickly.  You'll still probably need some sort of shuttle service for a wedding day but you'll save time which is priceless.