Incoming wall-o-text. Sorry
I agree with a lot that has been said here. You are playing Joel’s story and not a character of your own creation, so the choices made are mostly his and not yours. NG did a great job of investing the gamer in the characters. I wanted to save Ellie at any cost and, if the situation called for it, I wanted to hurt the people that hurt her. There was that one scene in the middle of the story where you getting into the city with their car and are ambushed. When that man grabbed Ellie I couldn’t wait to have Joel get at him. Now I don’t see this as “evil”, but just people protecting themselves and others in extreme situations.
A lot of people want to compare Joel and Ellies relationship as a father/daughter one, but it’s not completely that. Yes Ellie filled a space that was missing in Joel’s life, but it wasn’t a just as daughter or someone to care for. It was mostly hope. He wasn’t a completely terrible person before going on their journey, he was just lost in hopelessness which turned into toughness verging on anger and resentment (he isn’t fully there. His relationship with Marlene shows this). Ellie and not the cure is responsible for that new hope/meaning for him.
As for the ending I have to admit that I was a little conflicted. Killing the doctor was on the verge of unforgivable. But Joel didn’t want to be stuck in that hopeless again. I imagine that the internal conversation he has with himself was something like “What will I do if Ellie died. How will I go on”. Ellie was an important part of his life and he would not lose her and let her die. It is selfish, but a lot of what people do is selfish and Joel showed many times that he does put Ellies life before his and is prepared to die for her (the section where he is injured and goes looking for her).
Joel lying to Ellie at the end was also conflicting for me. But she did seem to know that he was lying and was ok with it. This was very important for closure at the end as if she didn’t accept his lie is would have been a slightly creepy kid-napping sort of situation.
As for the season change they couldn’t show you a full years worth of cut scenes and audiences today have moved past also needing a montage to fill in the blanks (that would have been super cheesy anyway). NG were probably confident even in their story telling that they knew people would fill-in the missing time spaces