IronArcturus: So you can rebind the buttons on X3 TC and AP?
Yes, in the more recent titles the options menu allows full customization, and even different control layout that you can save and load at will.
You can also do that in the older ones to some extent, but they are more limited in that aspect, so you'll need the help of some 3rd party tool to get a comfortable setup.
Side note:
since those are quite complex titles and a gamepad has a very limited amount of buttons, if you have access to a decent headset, you might want to have a look at some voice control software like VoiceAttack, GlovePIE or similar, which works great with this kind of games and it's also very immersive... you'll be able to assign unlimited command s and/or macros to a set of spoken phrases, freeing you few precious buttons on the pad for the very critical stuff.