I'm not sure what the first observation about playing as Sarah and Ellie really has to do with anything.
I think the observation is important too but there is a specific part that I haven't seen either of you guys bring up that might tie it all together and, to me, it answers this too:
What I'm not convinced on is that Joel has a progressive change in how he views Ellie, going from her simply being part of the job of smuggling to someone he genuinely cares about.
Bascially, the way I see it, the gradual change from "just a job" to surrogate daughter came at a scene right before Tess, Ellie and Joel got to the Capitol building. They are on a rooftop, I think, and they're all jumping down. Ellie had said something and right after that, Joel stared at his watch. It was a small thing but to me it said that Joel was thinking about his daughter and had started to draw similarities between his real daughter and Ellie. Those similarities are obvious to us as viewrs but it's not outright mentioned what Joel was thinking. Right after, that Tess looks at Joel and although it's not specified, I think she knew what Joel was thinking because she told him to focus on the job.
From then on out it was not really addressed in any clear or specific way that Joel started to care about Ellie because I think that we as viewers were supposed make that assumption given that probably anyone in Joel's position would probably form an uneasy (uncomfortable) attachment to someone that bears so many similarites to someone important that we have lost and never really gotten over. To me it was something that we were supposed to guess was going on in the background even though it wasn't addressed outright until the "baby girl" scene.
But this also lets me draw a few conclusions about Joel's personality and his motives for making the decisions he did at the end. Firstly, Joel, like most people in a post apocalyptic world, is filled with grief and pain that he doesn't want to confront. We know this because of the times when Ellie and his brother brought up the death of his kid. He couldn't even take an old photograph of his daughter because he couldn't confront it. Seeing this, it also lets me tie it into the fact that all through the game his progressive attachment to Ellie is hidden, because he's uneasy with it. Basically it establishes Joel as a person who has removed himself from emotion so that he doesn't have to deal with it.
That first point about his personality leads to a second conclusion I drew. Since he's so separated from the emotions he would normally feel, this has led him to take on a "do what needs to be done" or "it's either you or me" type of personality. It's the apocalypse they're in. It's established that Joel isn't associated with the Fireflies since he's not into any revolutionary activities and he's not pro-government either. He smuggles things on the underground to make a living, because that's what he has to do to survive. While doing that, he always confronts violent situations with extreme openness. He isn't fazed by the concept of murder or revenge and it shows because he doesn't hesistate in killing anyone at all in the most brutal of fashions. This is why he had absolutely no problem in killing the lady at the end despite her plea of being spared.
Was it selfish to take Ellie despite her being humanitys last hope and killing the scientists, absolutely. But to me the game isn't trying to justify it as much as it's trying to put you in Joel's shoes and show you what a person who has recently accepted his emotional attachment to someone coupled with a "you or me" personality would do in that position. I think the game and the writing did a great job of that and I absolutely enjoyed it. I legitimately felt what Joel was likely feeling at the moment he took her away and the moment he lied to her. It felt wrong, very wrong, but I think that's what they wanted you to feel and more importantly, understand.