We ate at both for breakfast in June.
The GF Cafe is light and airy and open. It serves traditional breakfast fare. Does not serve toast with the omlette. (Sorry, this bugged me, lol.)
It is a nice pleasant atmosphere with good food and decent service. Nothing about the food wowed us, but it was an good overall experience.
The Wave is a neat restaurant. It's enclosed, darker, no windows but a nice atmosphere. Very quiet at breakfast, as it was not busy when we went.
The food here is of a more natural, organic nature. Many healthy items are served on the menu. The Mickey waffles are whole wheat, they have sweet pototato pancakes. The buffet has many options, many different from the standard breakfasts you would find at other Disney restaurants that serves breakfast. You can also order more traditional items a la carte off the menu. I agree that the cheese grits are awesome!
Service here was good for us.
They are both good for breakfast, it kind of depends what kind of experience you want out of it.