Chuck E. Cheese -- they have more games that are physically smaller for the littler/younger kids. Plus, I like the fact that the kiddos get their hands stamped with their parents, with a number, they come in with. The stamps are checked when you are leaving to make sure the numbers matched. So basically, no one can leave with your child except you.
Other than that -- Gattitown is a buffet and Chuck E. Cheese is not. You order your pizza and they bring it to you when it is ready.