With Uncharted, the story is being a treasure hunter - not being a sociopathic killer. You have gameplay that doesn't match the story. There is no ethical questioning going on here.
Or like you've just absorbed bullets 19 times in the past stage and snapped the necks of a dozen grizzled mercenaries with the push of a button, but then an old man pulls a Derringer on you in a cutscene and your character just goes, "No, don't shoot, I give up..."
I mean, you don't have to be a softie to acknowledge that there's a truth to this, whether or not you're the type to feel it when you play your favorite games. The reality of the world these games are trying to portray often clashes with the mechanics of the gameplay you are in control of, and the more game producers focus on reality, the harder the clash can be. If you're supposed to just turn your brain off and play, then sure, nothing matters. But game campaigns have evolved to be "art" and the creators are putting detail and emotionality in them that they expect you to find value in experiencing, and ludonarrative dissonance is something that comes with the territory.
(Also, with graphics becoming more detailed, even if the story isn't connecting, you're still seeing more lifelike and relate-able characters/environments in them that you connect with unconsciously. That said, I wonder if there's a kind of uncanny valley or digital oversaturation we've experienced to combat that? There was a time when gibs and death animations were shocking and effective, when even MK1 was considered dangerous, but I don't think it's just that we've grown numb that these aren't a big deal anymore. I think we see so many digital creatures in our lives and are so aware that even millions of dollars of de-aging for The Irishman still feels inhuman that, despite massive improvements in character modeling and texturing, we just don't care if we see their heads explode. Contrast that with if you see a practical pumpkin-full-of-guts
head-pop in Scanners or
Rikki-Oh,
THAT catches your eyes and never lets go!)
You could look at something like Mega Man: in those games, the hero is a robot sent to murder his colleagues after Dr Wily has reprogrammed innocent worker bots to be bad guys. On paper, it's tragic... but in the game, you get supercool weapons every time you win and the stages are colorful and the play is great and they don't tell you a lot about the story outside of the manual and an occasional non-voiced cutscene, and so you can go 9, 10 games no problem of just slaughtering Robot Masters or, heck, everybody else you meet in Monsteropolis so long as you get cool gear after you've MegaBusted them. It all just goes together, and the game never asks you to consider much about the reality of what you're doing. Have fun, Blue Bomber!
If they did a game like that today, there would be cutscenes showing the backstory with Rock building Monsteropolis with friends, and there would be dialog of Mega Man shouting, "No, Cutman, don't make me do this!", and you would see the anguish on his face as he ended the first of many Robot Masters who were once just like him... and then you'd press Start and do it all over again.
Probably they WOULDN'T go that deep in a Mega Man game (they didn't during Powered Up, it'd be silly to really go there,) but that's what games like Uncharted set out to do. Games today are heavily into "immersion" and "reality" and "emotional impact." Uncharted is all about humanizing Nathan Drake (partly because, IMO, the mechanics are too basic to sustain gameplay without narrative, but that's a different discussion of how fun Uncharted would be without a story.) Lara Croft is just a tiger-murdering, back-flipping chick raiding tombs in the original games, but the more they humanized her, the more inadvertently they make clear that her adversaries are human (and they tried to battle against that by making bad guys really vicious and seem even rapey, but that just heightens awareness and makes it less "just a videogame".)