I think an FPS depends on the developer. For instance HALO on the Xbox has a great setup and interface using the gamepad. I didn't have any problem completing the game using the gamepad. CounterStrike on the Xbox is a different story. It takes some getting used to and I still suck at it.

Rainbow Six 3 works well with the gamepad and it's a pretty complicated game.
Medal of Honor on the Gamecube worked alright but the aiming was VERY slow. Morrowind on the Xbox works great with the gamepad. I couldn't imagine playing Age of Mythology with a gamepad though.