I don't think they ever explicitly confirmed that it's strictly all flying type Pokemon and all Pokemon with levitate ability.
Because it's going to be awkward as **** to animate Dodrio flying. I have a feeling it's going to be Pokemon with models floating above the ground. Because if you look, Salamence and Charizard are flying when in previous games they were just on the ground. They probably did that so they wouldn't have to make two separate models for sky battles.