I just have to weigh in here. As an air combat enthusiast and fan of ACTUAL flight sims like IL-2, Falcon 4.0, the MS Flight Simulator games and others, I really would never really want to use my flight stick for arcade sims like GSF or Freespace. I simply fail to see why one would need the fine control of a joystick when one doesn't have any wind or gravity or stall profile to contend with. In arcade sims, all you're really doing is pointing a cursor, not controlling an aircraft, and for me the mouse will always be superior to a joystick for that function. It's just faster and more precise.
Now I realize personal comfort applies here, because I guess many people who grew up on XvT and other classic space sims are more used to the joystick. But, just to give my view on things, I have tried playing games like Battlefield or Planetside with both a mouse and a joystick and I've always felt that, as long as you didn't have any 'realistic' flight characteristics to deal with, it's much easier getting your crosshair on target with a mouse.