Personally, I would choose IOA, but it depends on what your kids like.
I think IOA has more child-oriented attractions than USF, there is a Dr Suess Land and a Jurassic Park land which have a lot for kids, as well as a Comic book land complete with a parade of all the popular superheroes, as well as a really neat Spiderman ride. There also is a roller coaster in one of the lands (can't remember the name or the land)that is geared for kids. Both my 10-year old nephew and 3 year old son prefer IOA.
USF however does have Barney show, and in the same area there is a childrens roller coaster, the ET ride, and the Animal Planet show. MIB is also good, but there is a height requirement. Some of the other attractions like Twister and Earthquake are pretty realistic, so can be kind of scary for kids.