I have waited for this game for seven years just to be disappointed. What was the point of making the gamer fall in love with Ellie and Joel's character just to be informed that they are the bad guys. This story makes their story feel like it never happened. Everything we enjoyed about the first game was false. It feels confusing to say the least.
The game is really beautifully done (the enivorment, characters) but the story made no sense and you almost feel betrayed by the writers in the end.
I think the story should have been about Ellie getting word there was someone else out there like her who was immune and they needed help because they were captured by the seraphites. Joel could have joined her in some of the quests but he would stay behind due to an injury. So maybe Ellie meets someone like Lev that helps her on her path to rescuing someone who is immune like her and maybe the twist is it is her long lost sister or brother.