SPOILERS. After playing through the entire game and thinking about all the choices the devs made. I overall really enjoyed playing through this game. I believe Naughty Dog created another master piece. I do have some gripes with it though. I think that they should have moved around the timeline of some of the events making it flow better in the game. Right away Abby is established as a cruel character that seemingly did what she did even after being saved by Joel and Tommy. If the devs would have went through her backstory a little then she could have been a more likable and redeemable character.
Ellie's backstory parts could have been moved up more as well to get the impact of the murder to have more effect. It felt like her first bits of backstory stuff in this game was to explain new things Ellie can do like swim. Don't get me wrong, I loved Ellie's backstory parts in the game, I just thought they could have been moved around a little.
And to the people that still fight over The Last of Us 1's ending and say Joel is a bad person or a good person, You don't really use vaccines on fungal infections like the infection in The Last of Us, what the doctor should have done is monitor Ellie's antibodies and help other people build immunity through her antibodies. Killing her would be the worse possible thing that doctor could do. Abby's dad just wasn't really that smart.