I find the controller to be way more work than it is worth in shooting games.  With a mouse it only takes a split second to line up your shot, with a controller I have to fiddle around.  It's an endless cycle of trying to get that crosshair over the enemy, it skips over to the left, I try to nudge it over to the right and it goes too far, so I have to move at the slowest pace until it's lined up.  Might only take a second or two, but the frustration just adds up after a few enemies.
This isn't true for games that were designed for the controller, because they just aim for you.  I was watching a mate play Red Dead Redemption, GTAIV and CoD the other day and I couldn't believe how little input he actually had.  The crosshair snapped to the enemy upon aiming and just tracked them, for me that is a real immersion killer.