Definitely multiplayer. I spent countless ours playing four player splitscreen on Metroid Prime 2, and not being able to repeat that on Metroid Prime 3 was a huge letdown. I wouldn't mind co-op if it was optional (meaning that no stupid A.I. would take its place in single player) and didn't affect the level design too much.
I also wouldn't mind if they used dual analogues rather than motion controls. Accuracy







