Via Napoli and Coral Reef have been great with our toddlers at Epcot. I don't love magic kingdom dining but Liberty Tree lunch the best bet IMO. At hollywood studios, Mama Melrose is good. And I know it doesn't get a whole lot of love, but my kids like Rainforest Cafe at Animal Kingdom.
As far as the resorts, Trails End dinner and Boma breakfast are my two favorites for the family.
Don't feel like you have to do character meals just because you have kids. We find them loud, expensive, not relaxing at all, and generally not great food. I know people say you pay for the "character experience," but you can find most (not all) of the characters around the parks and if you plan strategically, you can see plenty of characters without much wait at all.