Man, the biggest question left up in the air is if Ellie ever knew at any point that the "cure" was a death sentence for her. As she says, she's pretty much felt that she was meant to die from time she was bitten and her friend died. So either way it wasn't until near the end that she realizes she has the choice to live. So she accepts the lie for Joel and for herself, I think. I debated it but I don't think she does so just for Joel's sake. Her journey then is her acceptance of the fact that she gets to live when her friend did not.
And of course, attachment is the biggest theme. Thus the Darth Vader joke - fuck the world, I'm saving the person I care about.
I hope that made sense. A lot of alt tabbing at work, heh.