I understand V.A.T.S. this way:
Most RTwP systems limit the unbalancing effect of pausing by keeping the turns from their parent turn based system, but having everyone's turns occur simultaneously, at regular intervals. When you pause and choose an action, that action waits in a queue until the next turn.
Fallout 3 ditches the turns and gives you a continuously refilling store of action points. You wait until the bar gets high enough, and then you pause and choose your action, which occurs immediately. All NPCs are acting in real time.
This makes sense for a single-character game with a focus on ranged combat, because it allows you to choose exactly when and where to attack. It would be impossible to use cover sensibly if you couldn't predict when your gun would go off. The system would be fiddly and irritating if you had to keep track of six people's AP bars and explicitly order all of their attacks, but that's not an issue here.
But! You can also attack while unpaused, if you aim the gun yourself. I suppose this would serve as the equivalent of X-Com's interrupt shots or DND's attacks of opportunity. It has the side-effect of "dramatically" slowing your AP recharge rate.
I can only think of one reason to have one combat mode impede the other: to force the player to focus on one or the other. If I'm right, that means it's possible to focus on V.A.T.S. and use it more or less exclusively. You move around in real time, but you can let die rolls decide the outcome of your attacks; aiming is optional. If someone happens to wander into your crosshairs, you can choose to take the shot, but it means a longer wait until your next AP attack.
On the other hand, you could just run and gun, occasionally pausing to go into your inventory or try out a disarm shot.
Sounds plausible, right? I wish someone would confirm it.