My 2ct. as a happy, casual-y gamepad pilot - There are two things I feel are relatively small tweaks that could improve my experience a lot:

1) The possibility to use controller keys as modifiers (e,g, right sholder button + X or Button5 + Button2, just like for example shift + m). At the moment it seems only ctrl, shift and alt are possible modifiers, and it only works with certain keys. Not sure how difficult it is to implement, but it seems rather simple in theory. As it allows to get rid of the keyboard I think this may also be of interest for joystick users.
In connection it'd be nice if it I was able to remap -everything- freely. As I use the right stick/IR for looking around I would very much like to map other things on my d-pad, but I can't seem to do so.

2) Input curves. I am probably not the first one to note this but it'd be very nice if it was possible to modify the input from the game side. Because of short controller sticks >> small lever, small precision movements become a chore. Changing the sensitivity helps but as of now there is no balance between the necessary responsiveness in battle and graceful steering in calm situations - on the pad, after a while, the tiny corrections for wind etc are uncomfortable for the thumb (not an issue with a joystick where you use your arm/wrist more). It'd be perfect if I was able to tweak it towards less sensitivity in the center and more towards the outside. For gamepads there are few tools available so it'd be a big help to be able to modify it from the game side.

I realize my minority position here so I certainly don't expect implementation. But as I believe there are few gamepad users here maybe some support may help sell a copy or two to more casual players.