Just finished the game. I can see why some people have had negative reactions to the storyline. The point is that it's supposed to make you uncomfortable, this isn't a world with clearly defined heroes and villains. The characters are more complex.
SPOILERS
Seeing a lot of criticism about playing as Abby. Initially, I agree it was difficult to relate to her as a character after playing as Ellie, but humanizing the "enemy" made you reevaluate what was really going on. It's basically the last moral dilemma of the first game, but spread throughout the story.
Overall upon finishing I was left conflicted, something no game has done to me before. And that's great, that's the point. This game gets you really thinking.
Also, props for the Rat King under the hospital. That's a disturbing enemy to fight. And theres a random bathroom (cant remember where) where when you open the door an infected gives you a jump scare. One heck of a fright! Haha