Controllers are good for platform games, but they died out when the dinosaurs were around, and are too imprecise for FPS use.
Thats why keyboard and mouse are used instead of stick control for aircraft, mounted artillery etc.....oh hang on a minute. Perhaps if Maverick had hit shift quicker, Goose would still be with us today.
The mouse serves a specific purpose in FPS games, with "games" being the operative word and that is to make reactions times faster than would actually be possible in the real world. I have the same argument with all the youngsters today that don't invert there sticks and claim it feels more natural, but it is only because that is what they are used to. At Mach 2 there is a reason you don't push forward to go up.
Controllers are more reflective of real world reaction times and don't require such well honed wrist action.