Controls are definately a matter of taste and you can, with practice achieve proficiency with any BUT one difference hasn't been talked about. I like a game to be immersive. I don't care much about competition, I want to experience the game, really get into it.
Lets take Call of Duty World at War, here I am and suddenly a pot load of enemy soldier come running at me waving swords and screaming banzia. OK I pick up my trust dual analog and dispatch them with my adroit thumb wiggling and button mashing. Feel real? Not really, I actually feel kind of silly. Oops, here comes the second wave only I will send these to meet their ancestors by wiggling a mouse and typing on a keyboard. Still kind of silly feeling.
Now comes the third wave only this time I'm packing heat. I've got something in my hands that looks and feels like a weapon and I shoot it by pulling a trigger. Now that's immersive. Hell, sometimes I'll duck behind the coach and pop up to give a quick burst. Or I can get more up close and personal by taking up my Perfect Shot which is a very nice pistol and feels good. Even the reloading motion feels right. Not only is it intuitive, fast, accurate, its also a lot more fun.
So you feel less silly holding a plastic toy gun and ducking behind the couch as if actualy in danger? Anyways if you can be immersed in something like a movie or book where you have no input, I don't see how a video game controler hurts immersion.
Well I tried using a real gun for a while but man, buying new flat screens was starting to hurt....
But the enjoyment?
Man, when I was still using real guns I just went over to a friends.