the basic engine in STO is the same as in Champions since they are both Cryptic games, the main diferences is the later code ontop, so the setup for the joystick/controller support just needed a bit of tweaking to get it improted into STO. I might work on a profile myself for my 360 controller at somepoint aswell for my fleet members and other to use if needed. if you don't like the ingame engine for binding the controls and want more indepth "layers" to the controler then I suggest going with
Pinnacle Game Profiler.