Well here's the thing. The Last of Us 1 wasn't all that remarkable of a game. However it told a decent story, with enjoyable characters. The game succeeds in making us enjoy the character relationship between Joel and Ellie. Everything else is basically window dressing to allowing the player to enjoy a relationship building journey. Which is why people love Ellie and Joel despite the fact they are obviously terrible people. It doesn't matter to the player by the end, because the building of the relationship between them wins the player over.
Thelma and Louise are shitty people, but beloved characters in cinema history because they are written so well. They have a genuine relationship and youend up rooting for them even though they are the bad guys.
The same thing in the first The Last of Us.
It's this relationship that people love the characters, and also why people are so upset that Naught Dog has decided that they don't give a shit about what they've built. They destroy the characters within the first 90 minutes of the game and the rest of the game spends so much time trying to break the characters people loved down, that it almost seems spiteful.
The conspiracy in me thinks that Amy Henning who refused to conform to Druckman's feminist ideals of storytelling got push out of Naught Dog. However she wrote a lot of the original Last of Us. After she was pushed out of the company, Neil tried to rewrite as much of her plot as he could, but too much of the game was already done. So a lot of Amy's writing remains in the original game.
Well Druckman holds a grudge because the original game didn't end up being what he wanted. Therefore with full creative control over Part 2, he did everything he could to make sure he SHIT on Amy's original characters and story. Thus all the disrespect to the characters we see through out the game. Hell characters talk shit about Joel 15 hours after he is killed. And the other character Ellie is just shit on the entire game. Why does Abby seemingly get all she wants, while Ellie's whole world is obliterated? Because Neil hated Amy's story. So fuck everything she wrote that the fans loved.