Rosh, I know you may wince at this example but in Baldur's Gate 2, you could still control your NPCs and they would still have side quests, talk to you, betray you, everything that a rounded charcter would do, etc. In Neverwinter Nights, you could control your one NPC to a degree and, in my opinion, those NPCs were one of the most well-rounded interactions (with their plethora of side quests and pertinent level ups).
Now, let me just expand my first comment. I'm not saying that the NPCs should be like those in Fallout Tactics in which you control every single one for every single action. And I never I wished for *direct* control of your NPCs. Falling back to the Baldur's Gate 2 example, your NPCs still could still act independantly with their scripts but you could move them aside or have them run away in crucial situations.
(snip irrelevent bullshit about giving commands to squadmates in some FPS with a single key and whatever)