I have some of my buttons swapped for Merc Kings using Steam's controller options and as a result trying to navigate menus is fairly annoying because I still use A/B from reflex then have to stop and remember to use the buttons I remapped the Jump/Roll actions to. (I use Jump=Right Bumper, Roll=A, Reload=B)

I know you can do this for keyboards, and I used AntiMicro to bind all my gamepad buttons to the corresponding keyboard keys, but that causes the game to register inputs from both the native gamepad and rebound keystrokes on certain buttons like Start (which causes the second player split screen window to pop in) so it's not really usable.