Is there any reason wireless controllers shouldn't work? I normally connect it in Xbox mode (it can pretend to be all three).
Edit: I figured out how to change modes while wired and it does work now. I'll post an update if I get wireless working.
None that I can think of- as long as they're xinput they should register in the first 4 controller ID slots that the game sniffs for devices on (0-3, reserved for xinput)
Okay, well thanks for your help anyway. I was having the same issue with Axiom Verge 2 and the wired workaround works there as well so I'm happy (the same controller works fine in the first game but not the second, its bizarre).