Honestly, I prefer controllers because I'm just better at it and it feels better.
Since I'm left handed I can never get the keyboard setup exactly how I want it, setting up the keys is always a pain, and I never remember how I do it from game to game so controls are always different from game to game.
It could be the little bit of auto aim most controller games put in, I don't know, but I just prefer to play the FPS with a controller.