Main Street Bakery. Good sandwiches and *amazing* pastries, and it is a good, quick option with kids who are anxious to get to the fun stuff!
Pinocchio Village Haus is good too. We usually share 2 meals (for 4 of us, 2 adults, 9yo, 6yo) there, because they have pizza and salad combo meals that are plenty big enough to share.
We found both Pecos Bills and Cosmic Rays to be a little chaotic with the kids in tow (they were 4 & 7 on that trip). Seating seems to be more in demand at those two, though that could have been a matter of our timing, and the menu is more traditional burgers & fries type counter service. The fixin' bars are pretty cool and go a long way towards sprucing up what would otherwise have been just another burger, but it could be a hassle with little ones waiting.