In my opinion Joel doesn't change and him going out at the end without big consequences just makes the story unsatisfied. If characters make total selfish decision, we want them to pay for it. In Empire Strikes Back Luce goes to Cloud City, besides Yoda warning him, that he isn't ready to face Vader, He still fights him, motivated by revenge for Obi-Wan and the attack on his friends, and has to pay for his mistake with his hand. Not only have action consequences in the movie, the whole sequences was foreshadowed and therefore shouldn't be a surprise for the audience and Luke himself. He walked openly into it.
In the Last of Us the whole end of story comes as a big surprise for everybody. All the previous chapters in the story show us people and a world, which got corrupted, but still has human worth saving and not deserve suffering. Those people we as player want to protect and help, because there properly more out there, and all the horrible scum of people got punished again. Up to this point we are on Ellis side to help the word and she also seen to be even more encouraged with her sacrifice.
But it is Joel, who makes the decision for us and Eliie and therefore, and chooses his own happiness over the happiness of others. It is a complete selfish decision and he got no consequences for it! In the whole game he never suffers consequences for his decisions at all. All bad things, which happens to him, are mostly accidents or outside of his influence. Nothing comes back to bite him, he is like the child, who gets everything and get away with it. This makes the ending so unsatisfied. I want him to finally pay for his selfish actions. At the end i really expected something bad happening to him, like Ellie running away or even they fight to the dead. She might be mad at him, just isn't enough, to get away with destroying the last hope for humanity.
I also see those tapes, which hint at the non-function of the operation, meaningless and even a cop-out. They only sacrifice the action of the story-teller, are not foreshadowed and are actually meaningless. Joel deciding against humanity before getting the tapes. Good thing, he never can do wrong! Hell, those tapes even show, that Ellie can't be possible mad at him at end. Just let here hear them and she would be on his side.
Maybe in the sequel somthing happens, but the game need to stay on its own foot. It fails with its ending (like many Naughty Dog stories), even so building up nice characters. It also show problems in story-telling with games. Joel going against my decision, complicity alienates me from the game and the story. I thought i was Joel through the game. My action are his. But at the end i never was Joel. We have a story about a selfish guy, who turns out to be a selfish guy. Surprise!