I don't really think Joel saw Ellie as a replacement daughter. I don't think he would have allowed her to do so much if he saw her as a daughter. It was a guardian relationship; his job was to protect her. Then, yes, platonic feelings grew, but it was more about trust I think. Anyway, the end to me was Ellie showing her acceptance. She didn't believe it, obviously, but didn't fight it or make any attempts to go back. She wants to stay with Joel despite it all.