I used a controller until I learned about advanced PC gaming, up until then I hadn't bought any big titles on PC and that all changed with Battlefield 1942 and Counter-Strike 1.5. I haven't looked back after then, I have a gamepad for my PC which I use for games like Super Meat Boy, Braid, and Jet Set Radio but if the game requires accurate shooting, I use key and mouse. I recently played a game that had auto aim, for keyboard and mouse or controller. After playing a few minutes, I got tired of auto aim because it slowed me down. Auto aim tries to hit people in the body but if you have played kb&m for any extended amount of time you learn that body shots are boring and are a waste of bullets.
I got used to keyboard and mouse extremely quickly, that said, I probably used the game with the toughest learning curve, CS 1.5. If you want to get good at FPS keyboard and mouse, you can download lots of old freeware games that have solid FPS controls. Or buy an old Medal of Honor game (I recommend Allied Assault) and just play through the campaign.
My issue with these which is better arguments is what determines which is better? Joysticks are more common so more people use them, they often have auto-aim which is easier, but they aren't more precise. There is a reason Counter-strike/TF2 haven't been overly popular on consoles, the games require fast accuracy which aren't easily attained on a gamepad.
What is the argument trying to prove, keyboard and mouse are much faster than gamepads, but keyboard and mouse in my experience can have higher levels of mastery. Anyone who ever played with any CPL or MLG pros on a pub server understands that the keyboard and mouse is far more advanced.
If the console market ever starts using keyboard and mouse I think PC will be in trouble, since most games aren't allowed to be modded.