In a thread this big, this issue has probably been brought up at least once prior, but here's another pet peeve of mine:
Painful, Pointless, and Painfully Pointless Pacifism
So, some violent games present the option to go the less violent route - usually knocking your opponents unconscious rather than causing considerably more permanent incapacitation.
Some games do this in a matter that does not irritate me. Others, of course, do this in a manner that makes me feel worse about being alive. Still others have parts of their nonlethal systems that I enjoy, and other parts that I do not enjoy. I won't be taking the trouble to organize this rant for now, so if you feel like killing me, go ahead (but if you use the baton to perform a nonlethal takedown, I might be able to recover, and then edit my article into something coherent).
In Undertale, every single encounter is pretty much a puzzle. Either keep dodging attacks while performing your own until you've killed your opponent (the lethal route), or keep dodging attacks until you can figure out how to get your opponent to stop attacking you (the nonlethal route). Much of the game's combat is like this. It makes sense. It's simple enough (well, dodging what may very well turn into Touhou but with puzzle elements and a larger hitbox isn't easy, but the concept is).
In Deus Ex (the very first one, where everything looks terrible but in a way that still somehow strikes me as visually appealing in its own fashion), your starting equipment consists of (If I remember this correctly) a single medkit, a pistol, some 10mm ammo for the pistol, and a riot prod. The very first person you talk to (assuming you don't just rush straight past him) tells you to "stick with the prod" - and advocates the use of nonlethal force for much (I think actually all) of the game. There are other situations in-story that, in-universe (or if the player wants to roleplay as a good guy - Deus Ex is, after all, a roleplaying game), provide the player with a reason to follow the advice of using nonlethal force. Enemies have certain conversations with each other that, while simple enough, remind the player that those are people you're fighting. A certain conversation between a pair of parents reminds the player that even the enemies have family. The people who are known for killing everything are depicted as completely amoral. There's probably a number of other ways the game reminds the player of the nonlethal option, including gameplay. Going the nonlethal route isn't actually especially hard (unless you're trying to take down a Commando, but even then there's a trick that lets players put them on their backs/faces much more easily) - the stun prod, while being a melee weapon, will stun most of the enemies it doesn't knock out, and it can, if you aim for the back, knock out nearly every single enemy in the game in one charge. Enemies who are knocked unconscious will not scream and alert other enemies (as opposed to screaming the exact same way as the last thirty people did when you shot them in the back or brained them with a crowbar), and two weapons are, seemingly, specifically designed for use in tandem with the baton/stun prod (I'll tell you about them if you ask).
And no, it's not the gas grenades. I barely used those things throughout the course of my nonlethal playthrough, in fact.
Anyway, in both those games, I found that going the nonlethal route was fulfilling story-wise, and, gameplay-wise, kept me on my toes, even if it meant I was denied some of the cooler, more lethal options.
Metal Gear Solid V's nonlethal system... Well, there were certainly many ways to take down targets nonlethally. However, I would usually pick one of two options:
Shoot the target with a tranquilizer gun or other nonlethal silenced gun
Approach the target, perform a quick dive to knock them down, and then aim a gun at them to perform a hold-up.
There were lots of other ways to take down targets nonlethally, and I think the presence and existence of riot suit soldiers was an attempt to make me use those methods... But much of the time I'd forget to use them. The base building mechanic is a good incentive for nonlethally killing, but it doesn't make me feel even remotely morally justified.
What a shame.
And, lastly in my list, Alpha Protocol.
There are a few perks and bonuses you get for performing enough nonlethal takedowns, which is a nice bonus (and the kind of bonus that doesn't really appear in the other games I listed). A build that would be strictly nonlethal would, I imagine, likely involve speccing into Pistols, Stealth, and Unarmed.
There are missions where killing enemies will have repercussions - attracting unwanted attention, and the like.
Other than that, though, nonlethal play limits one to options that, to me, aren't all that fun. They usually consist of "crouch-walk and then punch someone" or "shoot someone with tranq darts until they fall over".