I have a Saitek X52 Pro Flight Controller (from Saitek)

Apperently most of the buttons can't get recognized by the game (same with ArmA 2) and I guess this effects controllers in general.

But it would be really nice to get all buttons recognized.
Currently you need the delivered Controller Software and define any keyboard keys and bind these again In-Game.
But this makes it a bit hard, since then you have to bind multiple times the same key for certain actions. (R for reload / R for Countermeasures for example)