I don't want Joel and Ellie to be in the main game. I suppose they can be cameos, but their story is finished. It was left purposefully open, and Naughty Dog doesn't need to revisit it.
I want the main character to be Ish. Since he, like Tommy, is much more idealistic than Joel, and since he has a very tragic backstory, I want his story to be about a descent into despair and redemption.
I think the only major change since the first TLOU is that the Fireflies should be mostly gone as a result of Joel's actions. I think it would be interesting to see what would happen to the world without the hope that the Fireflies will bring it back to normalcy.
I think a prequel would be the worst thing to do. It worked with Ellie, because Left Behind was short and because her relationship with with Riley showed Ellie in a completely different light. I simply don't think there's enough to make a prequel compelling.