I've played FPS games on both.
Seriously though.
Try to use a controller on a PC shooter. You will miss because it lacks auto-aim.
Don't try to deny this. I've played console shooters on a regular basis. Several of them. They auto aim, and have awkward controls.
I don't even see how someone could say using a keyboard and mouse is bad, unless you were playing a game that wasn't a shooter or MMORPG.
Seriously. Motion-controlled mouse or pressure-controlled stick?
I'm going with motion, because that's how people move. It's natural. It makes better use of our co-ordination. I cannot see any faults with using a mouse.
A keyboard? How can this even be remotely uncomfortable? It's gotta be the most laziest and easy to use device ever used for gaming. Especially for FPS games. 1-2 fingers for WASD, you rarely ever have to hit any of the other buttons at the same time.
The only kinds of games that I'll prefer a controller over a keyboard/mouse is action/fighting games. Like BlazBlue or Dynasty Warriors. Or old-school games. They don't feel right without a controller.