The only real issues I had with the story were:
Ava. Don’t think I need to go into why. It’s been done to death.
The twins. There was just some stuff missing in the game to really make them compelling. Hints that there was more, but for some reason was left out. They felt incomplete honestly and that made them feel extremely one dimensional and annoying.
Siren power inconsistency leading to ludo-narrartive dissonance. Siren’s as portrayed in this game, especially Troy and Tyreen are ridiculously overpowered to the point of destroying even previously established canon. Lilith moving Sanctuary took a lot of Eridium and left her drained after. Meanwhile, Tyreen ports armies around like nothing and Troy can apparently phaselock Tannis from “out of nowhere”, leading to Tyreen teleporting her, without being anywhere in the vicinity. So why didn’t they do that to the VH and drop them into deep space or something? If they can literally lock and port people from miles away, the VH shouldn’t have a chance. Seriously, a girl and her robot shouldn’t be able to do anything against them. And more importantly, why can’t Amara? It just didn’t make sense.