This thought occurred to me while playing CP2077, but it's prevalent in a TON of games - instant kills by sneaking up behind enemies.
I usually play stealthy if given the option, I find it more fun than just wading through people in an ocean of blood, but this mechanic is almost game breaking in most places it appears. No matter how outgunned you are, all you have to do is wait til the enemy NPCs backs are turned for an instant, low-risk kill. Sure, some games make you grab them first before the kill, leaving a slight window where you can be spotted by another enemy or whatever, but with the tiniest modicum of planning that risk is almost nil.
In the case of CP2077, the stealth kill is available right from the start as well, so for someone like me who likes to play the stealthy way, there's barely any reason to spec into any other shit (except for the abilities which make it easier for me to sneak around dudes for the instant kill, lol).
If instant stealth kills weren't a thing, there'd be much more challenge in trying to ACTUALLY be stealthy, i.e. sneaking around enemies without killing/incapacitating them, completing your objective, then sneaking back out unseen. Of course, there are some games that reward this playstyle (MGS for example). But plenty of other games (including '77, not trying to dunk on it exclusively it's just freshest in my mind) will give you bonus rewards for "not leaving a trace behind" (i.e. not having a combat alert) when you've actually left a trail of snapped necks.
I don't really know what I'd like to see instead - I guess games where there's better application of stealth are usually ones that are designed with the stealthy playstyle from the ground up (the Arkham series, MGS). And I appreciate they're trying to give you a reward for creeping up on people, but like I said, it's almost game breaking with its effectiveness in most games. What do y'all think?
You might enjoy Invisible Inc. Most weapons only knock guards out for a couple of turns, and once they get up they'll be alert and actively hunting you. You can find lethal weapons but they're often more trouble than they're worth, they raise the alert level when you use them which often means more guards are called in anyway. You have to rely more on watching the guards' patrols, carefully managing your resources for hacking, and finding the right balance between speed and caution to get you through the level before things go haywire. It's different from some of the games you mentioned in that it's turn-based but it's definitely still a stealth game and I find that having time to contemplate how fucked you are as you weigh your options just adds to the tension.
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There's a setting where it can give you I think 5 days before the final mission. The expansion is also pretty good, and extends it with a tough midgame mission at day 3 and then a couple more days with a bit of a switcheroo of stuff after it, really gives it a better flow and your agents are completely insane by the end.