@ShaggE: Seems like I struck a nerve there. Defensive much?
But sure, I'll examine myself. I'm not perfectly rational about this shit as much as anyone. TBH I've probably tried to put words to something I can't properly articulate, so I'll moderate myself and try again:
Watching Vinny smash a random bystander's face in a car door is one thing, doing it myself is another. I find it physically uncomfortable to do that kind of shit. Is it funny to watch? Yep. Because it's fucking outlandish to me. It's dark humor on a level I can't personally execute. In the same way, since I started getting the feeling that Far Cry 3 has it "in" for animals, to be honest, I found it sort of darkly funny. My girlfriend asks what I'm playing and I answer it's an animal genocide simulator.
The argument that bothers me here, really, is the notion that hey guy, you kill people in games all the time, why does killing animals bug you so much, and I can't help but feel that animals are not even remotely in the same category. Perhaps I've simply become indoctrinated to think human beings are okay to maim because they're "us". It's like making racist jokes that concern your own race. It's okay then.
In the same breath, I felt physically ill in Splinter Cell Conviction when the game asked me to smack Grim around in that cutscene. I don't like the idea of punching a girl. Fallout 2, in Europe, didn't have kids in it. When I later heard the US version did, and had a "child killer" set of responses, my stomach churned a bit. In my broken little mind, kids and women are "not me", so it's not okay or funny to make violent, murderous jokes about them. I'm just not dude enough for that shit.
It does boil down to personal morality then. I apologize if I personally insulted you, that was stupidly defensive of me when I had my rhetoric challenged.
Maybe the question, in the end, is where player choice intersects the requirements of the gameplay. For instance, perhaps Far Cry 3 only really bugs me because it specifically asks me to kill animals I don't feel I should have to kill. You can't flip the coin any more ways than this; The crafting system in FC3 is pretty dumb. Can't sell shit because your wallet isn't big enough for the cash, guess it's time to run over some bull sharks in a speedboat! Gotta git that wallet upgrade!
So maybe it's the crafting system requiring me to do things that seem callous is what really bugs me. As for the hilarious killing of innocent bystanders, I'll leave that joke for you to enjoy.
But killing that turtle is going to stick with me for a while. Whoof.