Fainting and actual Pokemon death in this game
Pokemon can roam around on their own
Characters are teens
There is a Pokemon virus
Big Team Rocket conspiracy
Losing to Team Rocket has them inject you with the Pokemon virus, where you become a servent of them forever (?)
Speed up button, but hopefully not needed, as battles will be redone to be more fluid. Train your own Pokemon against themselves, too. Faster battle start animations. Fight money is determined beforehand in trainer battles outside gyms
Strong attacks on weak Pokemon can kill them, unless the strong pokemon has a good bond with the trainer
Bonus stats if you evolve your pokemon at certain minimum bond levels
Equippable item button. Like modern games, you could equip a fishing pole so you don't have to keep going back into menus to select them again.
Redone character evolution trees + moves + types to be more logical. Everything will be more thought out.
More evolutions, more spread out.
As suggested by the titles, good and bad less distiguishable. As well, Rock will be more serious for a slightly older audience. Closer to high level conspiracies.