Breakfast at the Grand Floridian Cafe has been my favorite so far. Service is a little snooty, but the Eggs Benedict is divine.
Next for me, would be the Western Omelet at the Whispering Canyon Cafe in the Wilderness Lodge. Don't waste your money on the all-you-can-eat skillet there. The Western Omelet is outstanding!
My third choice would be Boma. The food is really good at Boma. For some reason, though, their chairs hurt my back and I cannot get comfortable enough to really enjoy my breakfast there.
I loved Ohana's and 1900 Park Fare for the character breakfasts. Chef Mickey's was cute, too.
And I am really excited to try The Wave for breakfast. I hope the experience lives up to the menu.