The game shouldn't need to be analysed to death to understand it. None of it stands out as "wtf this doesn't make sense".
Here's a comment from someone I read:
"One observation, the first and last characters you play as are fourteen year old girls (Sarah and Ellie), and the first and last times you play as Joel are when you are carrying one of them (carrying Sarah through the street or Ellie through the hospital).
Also, the one thing that drives home that Joel is taking Ellie to be like his daughter is when he calls her "baby girl" when he picks her up off the table at the end. He calls Sarah the same thing when he lays her on the bed at the beginning.
Lastly, despite what the people in the video are saying, I don't think Joel is the bad guy. It seemed to me that the world of The Last Of Us was created to essentially be the real world, plus 20 years after a pandemic. And if that is true, then the creators know that in the real world, there are no true villains. The world is not black and white, and no one believes that they are the "bad guy". So in the game, there are no bad people, just people doing what we would consider to be bad things. And Joel makes the decision I think literally everyone would have made if they had been through what he had been through. Joel is not the bad guy, or the good guy. He is just a guy. Just like the rest of us"
I highly recommend watching this, too. It's got a few guys that have different interpretations of the game. It's interesting to hear about how certain people thought differently about what happened. They also point out a few things I didn't even notice in the game. Very fun to listen to.
http://ca.ign.com/videos/2013/06/21/the-last-of-us-spoilercast