Ooohh man! For a movie, that I had total control over, I'd definitely try to plan it out super carefully so I could appeal to all fans, but since it'd be my movie... I still wouldn't sell out to everyone else.
First off, I'd like the art style to be Hayao Miyazaki/Makoto Shinkai with an inspiration from Final Fantasy. Storywise, I'd like to see the Death Egg come back and everything takes place on Mobius. The story would also have a Miyazaki style to it.
I've had this idea in my head, that the story revolves around a giant tree that's in pain and attacks anything near it. So naturally, when Angel Island flew over it, the tree shot up and anchored the floating island in its place (much like a tree house). I'd play around with that idea, but have familiar Genesis levels make appearances. Also, I'd include characters from the games and comics/SatAm
And for a villain...MECHA KNUCKLES! (not the main villain though)
One day I'll probably write a story based on this