This game is GOTY for me and I'm now left with that awful depression you get after finishing a great book/movie/series. I also feel depressed because I think it's going to take a while before I see another game with this level of writing. Most of the positive stuff has already been pointed out, so I wanted to mention something I feel was a bit negative.
The game should have been shorter. I think the current standard of length/playtime for AAA-games is almost always detrimental to the narrative integrity. This is especially apparent in a game like this where the quality of the writing is so high. How many times in this game do you use specifically a ladder, pallet or a wooden board to solve environmental puzzles? Or the ridiculous amount of enemies you have to kill or stealth through during this game. I'm not saying that if they added more varied methods of puzzle solutions (other than pallets etc.) it would be resolved, but that almost all of these game mechanics/conventions appear in such systemic repetition over such a long time that the game and the narrative begins to divert.
The mechanics do have narrative resonance (or whatever you call it) by instilling that survival mindset/instinct (e.g. desperation ) in theme with the story. But I feel that it didn't evolve past that. After that, the design begins to become so transparent through systemic repetition - the mechanics and the narrative starts to divide into two seperated parts. I just don't think the narrative can endure 15 hours of this. In the end I felt like the gameplay and the narrative were two different components created by two segregated groups with only some occasional high-level collaboration. I did not feel this at all 5-6 hours into the game. It took about 6-7 hours before the gameplay started to "sabotage" the narrative experience. The mechanics/verbs didn't really have, or create, enough elasticity (?) to prevent this.
(caveat: most of the encounters were really well designed, i'm not arguing against that. I just, personally, have a very low tolerance for repetition.)
It's not uncommon to criticize games for being artificially lengthened, but as better/more immersive the writing gets, the more difficult it is to ignore. This is why it bothered me a lot more with Last of Us than any other game.