My memory goes to this one moment in FC2 when I had gotten into a bit of trouble with a group of enemy NPCs at the trainyard. Like an idiot I rushed in thinking I'd flush them out with grenades, but they were too entrenched in cover and took me down without too much fuss. My partner came to the rescue as she had done a few times before; she pulled me up, handed me a pistol, did a quick visual/verbal check to see that I was fit to fight and we battled it out with the 10 or so remaining enemy NPCs. shit was on fire and things were exploding and people were yelling... It was glorious.
We whittled them down to one last man but I wasn't sure where he was and my companion was out of my field of view at the time. A couple bursts from a rifle rang out from behind me but I noticed my health bar was still intact. The last guy got a few shots off on my companion, and she was on the ground. O.K., no problem I thought, she had been shot down before. I quickly took him out and sprinted to my companion's side. I figured I would inject her with a syringe as I'd done before and we'd be on our merry way. I was SOOOOO Wrong.
When I came up next to her she was still alive but very clearly fighting for her life. I furiously injected syringe after syringe into her but the look in her eyes grew more and more fiery, her body heaving and moving in ways I'd never seen in a videogame before or since. Her eyes and her slightly agape mouth had this regret-tinged sadness to them, and for a moment I really thought I could see her reflecting on a life filled to the brim with violence and hate. It was clear to me after about the 3rd syringe that the effort was futile and she seemed to acknowledge the same. We exchanged uneasy glances and I(I, I) muttered under my breath "OK. This is it. I'm here for you." And then she died.
Honestly, the closest to this that I felt in FC3 was at the beginning when Vaas kills the main character's brother. I'll admit that it was an emotionally charged moment (thanks in large part to Vaas' voice actor) but when I took a step back and analyzed it, it was clear that I was steered to that moment, to that outcome, and really, to that emotion. And so it felt sort of fake.
On the other hand, the feelings of isolation, desperation, & just overall sadness at the human condition are VERY pervasive in FC2. There's almost a philosophical undercurrent to it even though the plot can be sort of "meh" at times. I think it accomplishes that through a thick atmosphere and game mechanics that facilitate these sorts of emergent (read lifelike) moments. Lastly, since virtually every action is done in real time with no loading screen, the sense of player agency is just astounding. I don't really know the main character's name in FC2, because he is me.
EDIT: Awesome Review link above, thank you. He pretty much sums up how I feel about the two games