SPOILERS ALERT: Please don't read it, if you didn't finished game.
At first, I want to say that I like this ending, it's a "open ending" It's a dark ending for good people. It's happy ending for selfish people like me. But there are only one thing that really not haunts me still is: can Ellie to forgive Joel, after she'll learn the truth sooner or later? Joel saved her, but destroyed the meaning of her life. Ellie lost her friends, she always had the idea that everyone whom she loves, dying because of her, so she wanted to redeem her "guilt", she is probably knew that she would die, but hardly she clearly wanted die for mankind. In fact they all decided everything instead her, about the surgery (fireflies), and about the salvation (Joel).
So what do you think: can Ellie to forgive Joel? After all what they did together, after all horrors what they saw together, after all pain what they felt together??? After this lies? White lie.
Personaly I've got a optimistic theory about this:
The last talk on the hill: Ellie told about that she thinks that everyone dying because for her, and that she has no more meaning in life because she can't atone her "guilt". Joel told her: "I struggled for a long time with survivin'...And you... No matter what, you keep finding something to fight for". He clearly understood what he had done. But Ellie knew what he means, she knew that the meaning of HIS life is she . Saying "Okay", after the oath, it's means the same, if she would said "I love you too". Only a strong love (fatherly) can make a strong man like a Joel, to make a false oath, and she realized this, she is not stupid.
Ellie didn't awake after she almost drowned. In the car she noticed that she wears hospital shirt, Joel said, "...drugs are still wearing off"". It's not difficult to her, folding 1+1. That is, she suspected that something happened with the Fireflies, Joel done something . Asking him to swear to her, she probably wanted to checked his feelings for her. Again she didn't get rid of feelings of guilt. Joel knew that she blames herself, and probably he wanted to redirect her hatred to herself to HIMself, to it ceased to torture herself, but it seems to me that Ellie's mental state becomes even worse, seeing what Joel ready sake to go, because he loves her.
In General one of the most controversial endings. But in any case, I am sure that Ellie will not making suicide, or run away from Joel, because she loves Joel, and she'll never make hurts him, in this way. The soundtrack in the credits named "A new beginning" And this music makes me feel optimism http://www.youtube.com/watch?v=jAaR1aT_YCA Maybe it's means that everything will be alright with those two?
I want to agree on this assumption.
I have acquired the grade of Master in The Last of Us story/character/game knowledge as I have played it through 9 times.
... I have no life.
Deep down I think Ellie knows something seriously went wrong with the fireflies.
Why prep her for surgey and then decide not to go ahead? Joel's claim that there were dozens like her does not answer this question.
Why not wait until she is conscious? Considering how dangerous it is to travel.
She asks him directly if he told her the truth about what happens, but she knows how far to push him.
All in all a beautiful ending.
The most funny thing that Joel didn't lied about the vaccine is a useless. It's true. But how he will proving it to Ellie? He lied only about how he leave fireflies lab (massacre).
Joel (the fireflies and everyone else) had no idea about the usefulness of the vaccine.
Some notes are contain hints that the vaccine is useless, okay, this is already offtopic