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.
I don't have the patience for games for games like Splinter Cell either (I find even the shooting parts slow and boring) but I find that you're exaggerating.
MGS5 had excellent non-lethal systems. It had fast animations, you could interrogate, use as body shield, fulton extract, knock out, choke out, hip throw them, throw them into other enemies. Manipulating with them was a very satisfying experience, and is a prime example for how smooth and slick enemy interactions should be done.
MGS5 sets a new standard for AI, and unlike Splinter Cell/Assassins Creed/Batman and similar games which have a modicum of ways to handle/kill/control enemies, they are mostly gimmicky or water down to contextualized button presses which is basically little gameplay besides the timing of pressing the button at the right time.
The tranq pistol and the slo-mo reflex mode in MGS5 had so much depth to them, and it was thanks to the AI how the game was able to shine above any competitor in this field.
Even so, MGS5 in other ways shares the offense with most of these games and what OP is talking about as well- When you kill hundreds and hundreds, you cheapen the impact of death and you become desensitized to it. It becomes malleable and boring. You just killed 500 guys, who gives a fuck?
In some games it doesn't matter. Just like in some Hollywood it doesn't matter. Crank, John Wick and Shoot Em Up are action escapist films of highest and most satisfying quality. They are kill porn bloodbath extravaganzas that celebrate the extinguishment of human life.
Same with some games.
But you have other games that try to tell a story with consequences and with believeable actors mimicking real life, and way to often they break the rules because they cannot move the plot forward or make engaging gameplay without making a few levels to the brim with conveniently placed bad guys looking at crates in fucking warehouses just standing around and perfectly speaking out loud about crucial sensitive information, while also leaving keycards and sensitive emails around everywhere.
Like sexualized characters, killing tons of characters just because the creators cannot write them off in other words effectively is just a proponent of the stories we mostly see in games. Why? Because 90% of all games revolve around the killing, elimination, deduction or similar. Be in jumping on shrooms in Mario or torturing people in Manhunt, most games revolve around the same concept.
Game developers don't know how to make Mamma Mia or Lost in Translations into engaging gameplay. we are still stuck in a quagmire pointing at moving at objects and see virtual blood appearing. or jumping on them. or driving them down. killing them in RTS games, fighting games, role playing games, whatever.