I hope you don't mind when I post my suggestions, although I'm not within the team.

My suggestions:
- Don't give the player all abilities at all times, restrict them to the use of items, and - as Ganderoleg suggested - to a sort of mana.
- I wouldn't restrict the ability to a change when on a surface. At least not at all levels. There should a special reason why the player is sometimes restricted to start the gravity change from surface only. Give the player the freedom to change the gravity within the air by the mouse, depending on the given items restricted in some way or free around the whole 360 txsmi suggested.
- For the idea of Ganderoleg for building the scene with several layers have a look for limbo http://www.limbogame.org/ as well.