Nothing beats a good optical mouse. Partcularly for FPS. Bite the bullet and give it a shot.
I like the Logitech over the MS mice. Also get a good pad, like a RatPadz, mouse surface.
I've tried several controlers (Thrustmaster, Nostromo, others) and they're more trouble than they are worth. They don't even work with most games. What's really sad is they still sell these controllers, but have not added game profiles for them in years.
Anyway, give the mouse a shot. It's by far the preferred method.