I mentioned this earlier, but this sort of inconsistency is what makes the writing subpar, or at least not as great as everyone thinks.
It's good for a videogame but shits the bed in terms of competition in another medium-- That you and the game (apparently) want to compare it to Moby Dick is a bit much.
As you pointed out -- One moment it's asking you to infer Joel's actions, the next it's utterly contrived, or has a pregnant lady climbing rope etc etc.
You really can't have it both ways and expect people to understand both sides --Unless you're writing to provoke which seems to be the case here.
If every time an inconsistency comes up it can be put down to what you can infer, then almost any situation can be rendered invalid, as it comes down to what each viewer brings to it and the backstories that they've made up themselves. So Joel has flipped character and is soft now -- and pregnant lady has been using Abby's steroids, blah blah. Still doesn't make it coherent.
They could have shown Joel's character changing, and made us feel that, rather than walking us around an aquarium for half an hour looking for a Moby Dick reference.
Sure, that was an interesting chapter....So looking forward to hearing Owens scintillating dialogue on my next playthrough ....I'm being too harsh, but that part of the game was dogshit.
The main problem for me is that really the basic plot (heart of darkness) has been done to death in videogames.
The first game gave you something genuinely fresh in that it started off as something you'd seen before that slowly revealed it's self to be a character study. This is almost the opposite.
LOU2's story is really nothing but a standard videogame plot padded out with exactly the sort of dialogue you get from that sort of game. Constant melodrama, dumb choices, No! No! No! the floor is caving in moments that ND have done to death. We've seen it before, and despite some of the writing being good and the worldbuilding excellent, it's still an extremely conservative game in it's approach to story.
If there is some sensible criticism of the story, I'd like to hear it as most of it just boils down to "I like it because" and then someone firing back because they've imagined something different.
If this game is as serious about it's goals as it appears to be, then it needs to be criticised as such. Things like overlength, reusing of tropes, redundant scenes and crappy supporting characters come to mind.
It's a horribly paced story that works as a game because you can take a break from it -- Now I'm not sure about you, but the only reason I was wondering how it ended was because of the first game, not because I found the story gripping or the gameplay was still thrilling me.