For us, a lot of it has to do with our plans for the day. I have learned the hard way that going out of our way to a resort that we are not staying in/near to have breakfast is a) a transportation hassle and b) a huge time killer on a park day. We really don't do that too much anymore. So that would factor in to my decision more than anything else.
Having said that, in the parks, our favorite is Crystal Palace. Lots of breakfast choices, fun environment, bright and pretty inside, neutral characters for boys and girls and you're right inside MK when you are done. We have done Garden Grill for dinner and weren't wowed by it, but I hear that breakfast is better. It's also another place that's more gender neutral and when you're done, you are inside Epcot right next to Soarin'. Epcot also has Akershus but it's all princesses and not sure your son would be into that. If you are in AK, Tusker House is another good choice. Hollywood Studios has Hollywood and Vine but I wouldn't recommend that unless your kids are into the Disney Junior characters. We found the food yucky and the place was dirty.
Outside of the parks, you have some good choices at the resorts (1900 Park Fare, Chef Mickey's, Cape May, Trattorio al Forno) but personally, I wouldn't go out of my way to do any of them on a park day unless you are staying in/near one. To each their own though.