****Spoiler alert****
They killed Joel in Act 1 after he conveniently forgot his nose for survival and instinct for a trap. They chopped off Ellie's fingers...then denied you the choice to decide the fate of the antagonist who caused this. Total rubbish, lazy storytelling dressed up as 'brave' plot choices.
Naughty Dog: For future reference, here is a basic outline for a more agreeable storyline. Continue the story of Ellie and Joel, new long term goal broken down into chapters, series of secondary antagonosts taken down along the way before final confrontation with the primary antagonist. The end.
See how easy that was? See how it didn't involve characters the audience cared about getting brutally beaten to death or getting fingers chopped off?