The fact that he thinks of her as a replacement for his daughter isn't obvious?
Actually I'd say the complete opposite is the case, considering Joel explicitly states, "You sure as hell ain't my daughter," in the farmhouse after Ellie runs off with the horse. And even after Joel has his change of heart, there's one moment where Ellie says she's sorry about what happened to his daughter and Joel gives a reserved thanks for the sentiment.
I'm still not convinced that he thinks of her as a replacement by the end of the game.
The fact that in his situation, the knee-jerk reaction would be to save his 'daughter' so he doesn't lose his 'daughter' twice isn't obvious?
The complete and sudden reversal of his character is obvious, sure, but it's not at all developed throughout the game (or if it is, it's certainly not done in an obvious way). It, as I said in my earlier post, came across as extremely illogical on Joel's part and poorly explained on the writers' parts.
I'm not sure what you're looking for.
Guess you didn't see this, then:
I assumed these viewpoints drew from specific instances in the game to come to that conclusion. I was expecting some level of analysis of the themes and character development to support the idea that that's how the ending should be interpreted.
Oh well.
I'm not sure how you could miss that.