I have big issues with how non-lethal takedowns and methods are typically used in games. In all games, going non-lethal is really annoying compared to just blowing everyone's heads off. It's a game, not real life. Don't make my trying to spare the virtual lives of my virtual enemies into a full-time job.
All the games which let you choose non-lethal vs. lethal are like this. MGS, Deus Ex, Splinter Cell. If you go non-lethal, you have take the guy down, and then hide him or else someone might find him and wake him up, which requires you to slowly drag him into a closet to stuff him inside of while another guy might find you while you're doing it, and repeat forever. Fuck that, I'll just headshot everyone who gets in my way so I can move on. I have a game backlog a mile long, I don't have time to babysit every unconscious virtual mook I non-lethally took down.
Make non-lethal methods less aggravating in games and I'll use them more.