I'd like to see the HMs turned into key items instead. (eg. Flashlight, surfboard, machete, etc.) The moves themselves can be turned into TMs. I'd also like to see more than one region in a game.
For plotlines, I'm sick of the whole, evil team wants to take over the world using legendary pokemon. I kinda miss Team Rocket where the idea was just steal pokemon and make money. Something more realistic would be nice. I'd also like to see pokemon such as the starters on the cover again. And no more fighting/fire starters.
I like the idea of character customization and being the champion and being challenged after the Elite Four.
Additionally, I think it might be nice to have a Kanto or Johto remake, but with the storyline set some years in the future so you don't have to start off as Red for example. Now storyline, original region.