I'd love to see a story mode return, tbh. Subspace Emissary got mixed reviews, but if you don't like the story mode you don't have to play it.
As for characters, I'd love to see Snake come back. One Pokemon per generation sounds awesome as well. I want Generation 2 to have Pichu from Pokemon Trainer's team, Generation 3 to have Deoxys (I think one character for all of Deoxys's Formes would suffice), Generation 4 to have Lucario, Generation 5 to have Zoroark (or any other Unova Pokemon tbh - I'm not picky), Generation 6 to have Greninja, and Generation 7 to have Mimikyu.