Well I think it depends which FPS you are talking about. I was a huge Q3Arena player on the PC. Obviously I couldn't imagine playing quake any other way. Its a fast twitch shooter that you need a mouse and keyboard for. On the other hand I couldn't imagine playing Halo without a controller. I think the faster FPSs like Unreal Tourney and Quake should be kept on the PC while the console oriented shooters (Halo, Gears) should be played with a controller.
Yes Gears is a tps but its a shooter so i'm putting it in the argument.