Hwdareu87 made some good points, I think the ending is pretty good, it could've gone in so many different dirrections too bad there wasnt alternate endings.

I have to admit I was a little upset about breaking Ellie out of the hosbital. However, to see them two at the end and you get the feeling Joel has finally softened up is a nice ending...for two people. The fact that the cure for man kind could've been made is a little troubling to me, but as Hwdareu87 said man kind is pretty much all F'd up. As you get to experience in almost every encounter with strangers you are truley surviving because you cannot trust a single person.

I actually thought Joel was going to get infected though, when Ellie almost drowned at the end of the tunnel I thought he was goin to give mouth to mouth and then eventualy he would need to be put down. That would've been a big tear jerker...Sarah dieing in the beginning was enough of an emotional hit.