1: wings AU. There’s nothing much. Just Wayne having wings.
2: third planet AU. There were three planets swallowed by black hole, and three infants began their way to Earth. After events of the movie the third alien asserts himself as a villain. So Wayne and Megamind have to team up to save the planet. As war begins they discover their feelings for each other and purpose of life, and they get to know that new villain can actually hurt Wayne. So I imagined that scene when they realize Wayne is injured
Headcanon: during puberty Wayne discovers that there are small feathers growing out of his back. What is it? Disease? Mutation? Or maybe... mating mechanism?