My preference is usually turn-based. But I think it depends on the game, as well. (GTA probably wouldn't translate well into a turn-based game, for example. Though come to think of it, I'm still waiting for a good Car Wars port with all the tabletop rules...) Since FO3 it's pretty much just your one character (personally, I never had much patience for the companions in this game - they already have trouble following me around and I usually just leave them wherever they get svck after awhile...) I think it makes sense to have it real-time.
That said, I'd still like to see a modern update of a Fallout game with the party-based format and turn-based combat...
If you want turn based, use VATS.
Eh... not really. That's just fancy bullet-time, it doesn't do pretty much anything that would correlate to what I like about a turn-based game. I like VATS, but I like it as a cinematic bullet-time function.