Having grown up on Atari, NES, SNES, Sega, Sega CD, Gameboy, PS2, N64, Gamecube and finally PS3 and Xbox 360 ... I can safely say controllers are vastly superior to a keyboard mouse combo.
But really - in FPS there's a lot more to winning than just executing a headshot. I can guarantee you on Halo I never (well, rarely) sit still long enough for you to headshot me. A lot of it is simply how well you know your surroundings and the abilities of the weapons and character you are playing with. And on games like LOTR Conquest or Halo Wars I'm still much faster on a controller than anyone I've seen on a keyboard.