Having played more last night (though MUCh of my time was constantly remaking my character... still can't decide on my stats!) I can definitely say that you do a lot more damage via VATS than you do if you shoot them manually, but the amount of real-time it takes to kill the enemy probably works out to be about the same.

The big difference is that with VATS, you're saving a bunch of ammo and it doesn't lead to the seemingly-ridiculous situation where you shoot someone 34 times in the head before they die. In VATS, I've needed maybe 3-4 shots to the head if they're wearing some head armor... less if I crit.