Uncharted gets a lot of flak but how would you fix it? I'm not being facetious or combative here, I'm genuinely curious as to how you'd go about eliminating or minimizing LND.
1. Have Nate go pacifist and not kill anyone?
2. Change Nate's character so he's not a lovable rogue but a hate filled psychopath?
3. Have Nate wrestle with the idea of killing before every confrontation?
4. Have Nate be guilt-ridden/low health/low stamina/forced reluctance to engage in combat after a gun battle?
5. Turn Uncharted into a dream/simulation scenario?
6. Make all the enemies bloodthirsty puppy killers?
7. Make Nate fight robots instead of humans?
8. Eliminate combat altogether and just have Nate walking and climbing while conversing with companions for 10 hours?
All of those things makes the game sound incredibly unfun.
This is a solid post. I think that a lot of people take route #2, even in movies. It is a little weird, if you pause to think about it, to have Indiana Jones' hero theme swell just before a guy gets his head pulped by a propeller, for example, but it's not weird for a war boy to call for us to witness him just before he dies, all shiny and chrome.
But I'm not sure that going all grimdark and post apocalyptic, ala Mad Max: Fury Road, is the only way to go.
You can go completely in the opposite direction. Mario Mario is kind of a genocidal maniac, but his war crimes are presented in such an abstract and cartoonish way that not too many people seriously complain about them. But Uncharted doesn't really want to be that abstract, and I don't think that Drake wants to fight robots, either -- that route is always kind of a cop out.
I think that people are still figuring out how to do a swashbucklers in game form. Adventure games were an initial answer, but they have a whole host of flaws of their own. Firewatch experiments with letting a player explore an area in a non violent way, while still maintaining tension and interest, though there is not really any swash and buckle to it.
Real life combat is dangerous, but often not lethal for most of the people involved. There's a lot more suppressing fire, and attempts to convince an enemy to retreat or surrender, than there is straightforward slaughter. I don't know how you express those concepts in a way that moves like Uncharted combat does, though it would be interesting to see someone try.
Basically, I don't know. You pose excellent questions and there aren't easy answers. Regardless, the problem remains: there is a disconnect between the Drake in the cut scenes and the Drake in the game, and I think that it is worthwhile talking about that disconnect, and thinking of ways to do better in future games.
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Edit: there's also the "don't put stories in your games" camp, but I'm not sure that they're right, either -- it is fun to be able to play through a story, and it would be neat to hone our abilities to tell good stories in good games.)