That's Not For You To Decide.
It's very strange to go back to the Uncharted games after playing The Last of Us. The games share many elements, but they're utterly different in tone. In The Last of Us, killing people makes sense given the context and the character you're playing, and it's treated as brutal and horrific but unavoidable to survive. In the Uncharted games, you're loveable, good-hearted treasure hunter Nathan Drake and the fact that you kill thousands of mercenaries is cheerfully ignored.
(It's also bizarre that picking up twenty bullets at a time is a common occurrence in Uncharted. In The Last of Us, it's Christmas if you manage to find three.)
I suppose 'ha ha, Nate is such a charming dork, TIME TO KILL ANOTHER HUNDRED MERCENARIES' is the problem with trying to tell stories in a videogame. I'm a fierce believer in the narrative potential of games, but games do typically require some sort of gameplay, and sometimes that gameplay is at odds with the story being told. In lighthearted games like the Uncharted series, I suppose you sort of have to ignore the ridiculous amounts of murder you end up committing; it'll completely undermine the way the characters are presented if you think about it for too long. ALL THIS SHOOTING IS A METAPHOR FOR TRAVERSING TRICKY TERRAIN.
This is something that occasionally bothers me in Final Fantasy games, too; most of the games involve human enemies, usually soldiers of some sort, and it rarely seems appropriate for the characters to cut them down without a qualm. It's always a bit odd to think, Hang on, Snow Villiers seems like a really nice guy, but I just made him punch someone to death.
I'm sure there's a term for this clash between gameplay and tone/story/characterisation. Hang on while I look it up. Ludonarrative dissonance! That's it. Uncharted is ludonarratively dissonancing all over the place.
It's a tricky problem to solve. Not every game in which you fight people can be The Last of Us; The Last of Us is a wonderful game, but I wouldn't be able to cope with that level of bleakness in everything. So I suppose for the moment I'll just accept the fact that loveable treasure hunter Nathan Drake can punch some guys on a train to death and then quip, 'All right, boys, just needed to punch your tickets,' and I'll laugh and say 'Nate, you dork' rather than 'Oh, my God, what's wrong with you?'
After writing the above, I went off and finished my replay of Uncharted 2. I had forgotten how much I love the ending of that game! Nate/Elena continues to be one of my favourite pairings of all time, and their interactions continue to make me make absurd chirping noises. I also really like the friendship that develops between Elena and Chloe; I remember I worried when they first met that their dynamic would be rooted solely in romantic jealousy, so I was surprised and delighted that they ended up getting along extremely well as co-founders of the 'Nathan Drake Ruined Our Lives' club.
LET'S IGNORE ALL THE MERCENARIES THESE GUYS HAVE KILLED AND FOCUS ON HOW MUCH THEY DELIGHT ME.
(I had also forgotten how hot it is when Nate is stumbling around in the Himalayas, slowly bleeding to death. I'm an awful, awful person.)