The problem is that in TLOU2 the story is all over the place. Joel has lost all intelligence and spidey sense, which was demonstrated multiple times in the TLOU 1. Then you have the scars. I have no problem with LGBTQ community but what are the odds of a religious group coming together in a post apocalyptic era only hunt the LGBTQ community. I say 0. The setting in first game made sense, because it was always about survival first, now they added the scars which take up a huge chunk of the story only to talk about this issue. If they wanted to do that, there could have been other ways, this was not the right way as it just takes away from making the game believable. Finally the revenge cycle. So here's the deal, Abby and her friends killed Ellie's father, Ellie goes out seeking revenge loses some friends and kills many and when the time comes to kill abby she lets her go, to break the cycle. Really? When was seeking justice wrong? Its morally wrong. Joel did what he did to save his daughter, his motivations and his actions made sense. Ellie's not so much.
My final problem with the story is how there is no moral confusion in characters. In first game,you knew no one was good, no one was bad, it was about survival. We were shown joels dark side but we were given compelling reasons to love him. The problem in TLOU 2 is that ND has wiped the moral grey zone for good guys (Abby) and bad guys (Ellie). The plot no longer has the moral complexity that the first one had. They make you do bad stuff with ellie and good stuff with abby just to make you like her. It doesn't work.