Using V.A.T.S. has some serious drawbacks though; it's based on action points, and while the game does pause and allow you to let your character aim instead of doing it yourself, once you release the V.A.T.S., the action will continue, so your enemies will be moving and so on, and what's actually detrimental to you is the fact that you can't go into V.A.T.S. again, since you're out of action points.
Now you're left with having to fight in real time, but your enemy is already clawing your head off.
Also, V.A.T.S. doesn't give a rat's ass about the fact that your character may be shooting at the last pixel of a wall, instead of the intended target. It will still run through all of the actions given to it, and you've just basically killed yourself.
And finally, if your character's shooting skill is bad, V.A.T.S. is useless beyond three feet. You'll be getting shit like 23% to hit. Good luck with that. Meanwhile, you can shoot headshots at a mile if you've got the gear, regardless of your shooting skill. In Fallout 3 and New Vegas, anyways, which is obviously what I'm talking about, since that's where V.A.T.S. is from.