So I actually tried out RA 1&2 on my Mac mini. Seem to be working okay with my stick although the calibration is off. Even without that problem, I think RA 2 plays a hell of a lot better with mouse controls, although some of those vehicle maneuver missions can be a bit challenging. RA 1 would work great with stick if it calibrated correctly. The mouse controls for that one are quite horrendous in comparison.
By the way, did you actually set the controls to 'joystick' on the setup screen before launching the game? It doesn't work automatically with sticks unless you do that, since both games are initially set up for mouse-only controls.
Those are the only two games with which I have had actual calibration issues. I've played Wing Commander, Privateer, TIE Fighter, and Descent without any problems before. *shrug* Just tested Descent again, and no problems there, although I actually enjoy it more playing that one with mouse+keyboard controls.