For anyone still playing this game with a controller: does the controller work correctly for you when flying? I'm finding that driving on the ground or water works fine, but in the air the up-down controls don't work correctly. My ship will end up just climbing no matter what I do. I've tried turning on and off the "reverse flight controls" setting to no effect.
I've gotten the same problem with two controllers so it's not just the controller. Initially I tried it with a Stratus, which I ended up returning because it was too small for me. I finally got sick of waiting for a full size official bluetooth MFi controller, and jailbroke my iPad and got a PS3 controller. It works great in every other game but has the same problem when flying in this game.