I don't think I ever walked away from a game feeling more dissatisfied that when I finished The Last of Us. I was seriously in a black rage for hours after its completion, furious that I had wasted time on something that led up to a completely pointless ending. Frankly, it baffles me how anyone can possibly stand by the game or its protagonist, considering that conclusion.
I think that Joel is probably the most selfish, reprehensible character I've ever had the displeasure of playing as. He claims to care about Ellie, but in truth she as a person means absolutely nothing to him, just a way for him to live out a deluded fantasy that his own daughter never died. He kills for her, but its clear that he doesn't care in the slightest about her own choices or personality. She was willing to sacrifice herself to save mankind, and he stole her away, slaughtered the only hope we had left, and carted her off to a backwater town where she will likely die in a decade anyways. He's pathetic, and the only reason I didn't give up and stop playing during the fight inside the hospital was because I was praying that someone would kill him before he did more damage. Sadly, I was mistaken.
I've seen people hold up Joel's actions as somehow "moral" because they have some qualm with the Fireflies. How on Earth does that matter in any way? I don't care what the Fireflies have done. If they found a way to save mankind, I would support finding it. If the military found one, I would support it. If Joel's brother or the other survivors found one, I would support it, or if some crazed dictator found it, or bandits, or anyone else. Do billions of lives mean so little that they should be condemned based on petty political concerns? What use are complaints like that when humanity is on its last legs, and this may be the last chance to save it? This may shock some people, but the world does not revolve around you or your worthless political wrangling, and the fact that some people were rude or abusive to you personally means absolutely nothing when weighed against the good of others. I didn't care that some Firefly pointed a gun at my head or threatened me, because what anyone does to me is irrelevant if you weigh it against billions of lives.
"Mankind doesn't deserve to survive, so I'm going to deprive it of its only chance to rebuild and become better!" What insane kind of logic is that? You're saying that millions upon millions of innocent people deserve to die, and our entire species deserves to be wiped out, because some of them are bad? And because many were forced to do evil things because of the situation they were forced into? And now you're destroying the only chance to cure that situation, end the suffering, and help mankind heal? You're condemning people based on circumstances that you are allowing to perpetuate, rather than try to end them. This goes for the fatalist as well, who says "Well, mankind is doomed anyways, so what matter is it?" The only reason it is doomed is because of the choice you just made! It's because of people like that, who put selfish wants over the needs of others, that humanity is being exterminated, and now you say it is inevitable to cover your own actions? The fact that it was possible to make a cure proves that it was not inevitable, and that there was a chance to save everyone, but Joel chose to snuff the last light out. You can say that even then it isn't a certainty that we can rebuild, but is it not even worth trying? Do other people really mean that little?
Ellie had no problem dying to save mankind, so why should we? So far as I'm concerned, any man that isn't willing to sacrifice his life for others doesn't deserve to have that life to begin with. What Joel wants is irrelevant, what you and I want is irrelevant, and what the Fireflies or the military or anyone else wants is irrelevant if mankind goes extinct. There is no other concern. Ask the four billion dead people, or the two billion living ones in that world how much one person's desires are worth, or whether politics still matter, and guess what that answer will be.