All this sounds ace. Naughty Dog having a principal theme is...encouraging? I don't know how to describe it.The Last of Us was a game built on vignettes, so writing the script with a theme in mind probably helps with structure.
I understood Joel. I didn't like him. What morally redeeming traits he has are derived from his relationship with Ellie and Tess and even then he gets rough (such as the end of the 1st game). I think that's fine and dandy. But I hope they avoid turning Ellie into Joel 2.0. That's all I ask for.
I hope you can choose Joel when they are doing things together. I liked Ellie in the last game, but the fistfisting Joel had was an aspect that made him best for me. So I really hope we still get to play alot of him also.