Well, my family likes the Electric Umbrella in Epcot. Air conditioned, plenty of seating indoors, and the food is pretty decent. I've eaten there for lunch and dinner...not sure what they have if anything for breakfast.
Breakfast in Magic Kingdom is usually done at the Bakery on Main Street. They have great cinnamon buns, egg sandwiches, etc. There's limited seating inside, but they're also air conditioned.
AK - we're never there for very long, so we usually grab breakfast at a cart if we happen to be there during the breakfast hours.
MGM - I don't think I've ever done breakfast there, but lunch at the Backlot Express is my location of choice. They have a great portobello mushroom sandwich there that is phenomenal! They're open odd hours, so we typically head there for lunch to guarantee we get to eat there. And there's a decent amount of air conditioned seating indoors. It's kind of a little known spot, so we've rarely had trouble getting seating, even at peak times.