I enjoy story with my games. Games like Serious Sam never appealed to me, and I got bored of the multiplayer content of Call of Duty pretty quick; I was really only in it for the stories. Yes, I played the "No Russian" mission and yes it affected me, but isn't that what we play games *for*? To explore things we couldn't explore in real life?
I don't like the idea that there's no consequences for my actions. The games I've really enjoyed playing: Fallout, Fallout 2, Baldur's Gate II, KOTR, KOTR2, etc etc etc. Games where what you do matters. Games that allow you to force-push civilians off cliffs, but where there consequences for that which you probably won't like.
People argue about the moral issues behind putting killable civilians into video games. I counter that there's a moral issue with *removing* them. To display this false, clean image of war where everyone with their name in red is a bad guy and everyone with their name in green is a likeable hero really doesn't do it for me.
Things start to get ludicrous in games like Fable 2. A major plot point in your backstory is where, as a child, your character being almost killed by gunshot, but then as an adult the game won't let you harm children yourself. What the...? Surely the game designers missed a huge potential story arc here; if you kill a child, later, you could (say) have that child's ghost come back to haunt you in a dream. The ghost could point out the hypocrisy of what you've done, and remind you that you're now part of the cycle of violence -- child abusers were often, themselves, abused. This to me is far more interesting and thought provoking than "children are immortal, except when it's you, then it's fair game".
When I have kids, I want them to learn that there are consequences for their actions. No, I won't give them violent games before they're ready, but when they get old enough I will search out video games such as Fallout 2, Baldur's Gate 2 and KOTR 2 where the actions and choices they make affect them in the future, in ways they may find hard to see at the time.
That, I think, is a much better lesson for them than "KILL EVERYONE AND LET GOD SORT THEM OUT."