The first reason Incredible Pizza is so much better than Chucky Cheese is the pizza is much better. It's not fantastic pizza by any means, but it's good pizza and that's something Chucky Cheese cannot claim. They've also got a great salad bar and a large variety of pizza choices (including mac & cheese pizza).
The second reason is that they've got the space to make a truly fun game room with games, rides, go carts and movies. I'll take my son here rather than Chucky Cheese any day.