I didn't like the ending of The Last of Us. There are tons of threads rehashing this ad infinitum and I don't want to get into the specifics of the story choices, but what I felt most of all was that it showed one of the principal reasons that so many game stories are bad, which is the limitations of gameplay. Once Marlene tells Joel that they're going to kill Ellie to operate on her there are a thousand ways he could have reacted in a movie or a novel or whatever. He could have tried to reason with the Fireflies. He could have asked to see Ellie one last time. He could have claimed to have information from the lab in Colorado that would enable them to get the vaccine without killing her. He could have tried to take Marlene hostage. Whatever.
In a game, with a limited engine, there was basically just one option. Kill/Sneak through an environment of chest high cover and side rooms to save her.
I personally chose to go the violent route, mostly because I liked clearing areas to search for loot, and because they gave me an assault rifle and am I supposed to NOT play with the only automatic weapon in the game and force myself to sneak around? Maybe, but that's the tension. Do I want to have fun or do I want the game to tell a consistent story? Sneaking also felt inauthentic because she was already being prepped for surgery, so if you are going to get there you better get there as fast as possible.
So there I was again at the end of a game playing a cover-based shooter where I gun down lots of men to advance towards my goal, and honestly it reminded me a lot of Spec-Ops: The Line, except that the ending in that game is supposed to show your character's insanity and depravity while in The Last of Us you are supposed to empathize with Joel, at least to some degree. I don't think the games are meant to be similar, but they are constrained by their mechanics and forced into similar situations. The big difference is that Spec-Ops leans into its mechanics while TLOU still refuses to acknowledge exactly what its character is doing. TLOU was meant at least in part as a reaction to the criticism that Nathan Drake is a jaunty psychopath who murders hundreds with a grin on his face and a spring in his step. Joel is supposed to be a more reluctant and guilty killer, forced into it not out of a desire for treasure but a need to survive. The game is meant to play into this by offering stealth as a real option and using scarcity to make killing not always the best option*. Despite that I found myself at the end of a game killing a bunch of misguided-rather-than-evil Firefly soldiers, husbands sons and fathers, because that was the only choice the game really gave me.
It's clear that TLOU's programmers put a lot more focus into combat and fighting than any other part of the gameplay. The puzzles are rudimentary (Find wooden pallet. Use wooden pallet to cross water) and the traversal is fine, but like every game it's inconsistent what you can climb and what you can't, you can't stack things to create structures to climb on, and it's rarely "fun." The engine just doesn't have a lot to offer there. I actually think that the puzzle with the broken ladder you do right before you get to the hospital, simple as it is, is an example of how the game could have focused more on traversal and moving through an environment, which would have resonated with the themes better than, say, the last big pack of infected you fight, which is so easy at that point that I almost felt sorry for them as I picked them off with arrows and molotvs.
As long as the people designing the gameplay parts focus their time on killing, games will inevitably have to tell stories about killers, and nuanced stories like TLOU's will always be in tension with the gameplay. Overall the Last of Us had a very well-told story, good characters (except for David, what a cartoonish villain) and I even enjoyed the gameplay, though others didn't. But it didn't rise to the level of a great movie or book because it couldn't transcend what you actually DID in the game. Which was kill people. And collect comic books. And swim around with the same wooden pallet like 5 times for some reason.
*though it undermines that by putting collectibles and environments that are much easier to explore once the bad guys are all down.