At MK, what about Pecos Bills? They have mac and cheese and uncrustables for picky kids. I think my picky eater had a cheese quesadilla here, not sure if you can still get that or not. I really liked the salads and since you add toppings yourself, you can minimize the less healthy stuff. Some of the best counter service options are at the resorts outside of MK - love Contempo Cafe and Captain Cooks. In Epcot we have eaten at Liberty Inn (I know so many great choices, but my picky one picked this place). They have more options now and the salads and grilled chicken sandwich were pretty good. I also like going over to Boardwalk Bakery for sandwiches/salads. I've gotten my picky guy pizza at the take out window right nearby. HS is the tough one for us. We usually eat at Fairfax Fare/Rosie's for the BBQ and chicken nuggets for my picky guy. At AK, my picky guy ate at Starbucks (he loves the bacon gouda breakfast sandwich)! The rest of us split the hummus/veggies, cheese and fruit, and some fresh fruit. It was way too hot to eat a normal meal there.
I often order of the kids menu to make it "healthier". The serving size is smaller and it comes with choice of two sides which are things like carrots, apples, grapes, small yogurt, or apple sauce. I look for places with grilled wraps, salads, turkey sandwich, etc. as entrees on the kids menu.