In MK, we really like Columbia Harbour House - the seating upstairs is so nice & relaxing.
At MGM, we like Toy Story Pizza Planet.
At EPCOT, there's also Sunshine Seasons in the Land Pavillion.
(At AK, we eat at Flame Tree, but the seating is outside. We get the kids Happy Meals from Restaurantasauras, and I think the seating there is inside.)