In the Magic Kingdom, with two small kids, I would head to Columbia Harbor House. They have good food and they have ample indoor seating. Gotta love that Air Conditioning or Heater, depending on which type of horrible weather Orlando is throwing at tourists that day. Get seats upstairs for a quieter dining experience and more choice of seats.
Epcot's Sunshine Season has great food, but I find it rather noisy, crowded, and sometimes difficult to find a seat. I adore the vegetarian plate at Tangerine Cafe in Morocco.
DHS means a trip to Starring Rolls for our family, but beware there is only outdoor seating and it is nestled next to and beneath a smoking area, which is a huge trigger for my asthma, so often these meals get lugged elsewhere in the park to enjoy.
Animal Kingdom requires a trip to Flametree BBQ and following the seating trail all the way to the water's edge to sit in a carved and painted pagoda and enjoy the view of Everest. Note, there is a place in the seating area to get sauces, napkins, and such, so don't feel you have to get all of those piled on your tray and balance them all the way to the eating area.
Downtown Disney hosts Wolfgang Puck Express and Earl of Sandwich. We find Puck's easier with small kids since they bring the food out to you and refill your drinks, which makes dining with children a lot easier.
As to the water parks. The Donuts were amazingly yummy, fresh and tasty. I have never eaten a full meal there due to the way I visit the water parks, but my son really liked a salad he got there.