And they're usually shooting at you, or would be shooting at you if they saw you. What the hell do people expect Drake to do? "Bruh, I'm a pacifist, go ahead and shoot me"?
nathan drake's existence is strange. he is supposed to be an everyman, or at least super relatable, yet i have yet to meet a single person who graduated from treasure hunting college with a degree in treasure hunting after having written a thesis on treasure hunting. he's not indiana jones, a man who lives in a lost, more rugged time who wants to preserve history. he's not john mcclane, a man who has a lot of skill but is just in the wrong place at the wrong time. nathan drake is supposed to be somewhat goofy and a little roguish. he swings his arms wildly while jumping but is still a hit with the ladies and is quick with a quip. he's never in the wrong place at the wrong time because he puts himself in the situation he's in. he's hunting treasure presumably for himself, and the thrill of it, so he's not exactly relatable either (he doesn't exist in our world, nor would he as a normal everyman type).
he works better as a villain. he's actually way more interesting this way. imagine a globetrotting adventurer who kills everyone who gets in his way for the thrill of it while joking with his cronies at every opportunity. someone who doesn't think what he's doing is really all that wrong. that's a lot more compelling as someone to root against than someone i'm supposed to sympathize with, or influence their actions.
elena is the better everyman in the series. she has a more grounded reason for doing the things she does. an investigative journalist - fantastic! that makes sense in our world in how she might get caught up in something bigger than herself. she might even make weary quips about how she's way in over her head this time. of course, the game would need to be different too. the shooting aspect is a major distraction from what the tone is trying to set up. the games should be more puzzley and platformy with far less emphasis on direct human conflict. it would make the moments with people a lot more meaningful too.
that's what i thought worked well in the last of us. not only was joel unrepentantly a killer, it made sense. there was some added weight too in that we knew what could have led him to his life twenty years after the outbreak. more than that, the world is mean and ugly and everyone's against each other. so there it makes sense it's a shooter.