Now, you may have wondered why I have named this discussion after the (in)famous Bioshock 1 quote. Its simple, when gaming, have you ever felt like your character rally had a choice in their decisions, like, if you were in their shoes, would you yourself choose that decision? Or, are they merely a slave, forced to make that decision because of some outside force (That isn't the player), like, is everything they've done because the antagonist (main or otherwise), or to the benefit of some group. Are they really doing actions of their own free will, or are they just being jerked around by multiple factions? For me, yes and no. If I am aware that X or Y group is obviously, or subtly using me, I pretend to go along with it, and possible, either strike out as an independent, or choose the side that is the lesser of two greys, or lesser of two evils, as the saying goes. How bout you guys? Is your character a (Wo)man, or a slave?
I've always got characters in all the camps. There's that one character who is doing all the fetch quests, trying to please everyone, one who picks and chooses based on whose cause he actually cares about, and the one self interested character who doesn't even want to hear about peoples' problems. Part of the problem with the realism of it is that in most AAA RPGs, even your main questline quickly devolves into you getting jerked around by whoever you "side" with, doing literally all their dirty work. It's hard to feel like the character is doing anything for themselves when that happens.
Usually on my first playthrough of an open-world/multiple choice game I make my own decisions and will usually try and go against what the game makes me do, unless I actually agree with what it wants me to do. Then on my second playthrough I just do the opposite of my original choices.