I think that they need to make an M-rated Pokemon game. I know people would say that won't pander to the younger crowds, but the original people who played the original games are close to the age where they'd be in college, they need to bring those people back in if they want to make money.
Plus, I'm interested what they would do to make it M-rated, probably do something like a Fabled storyline, where the second half of the game takes place after completing the main story. (I've only played III, so if I'm wrong on the first two, forgive my ignorance.)
That, or they need to make like a Pokemon Rainbow, where all the generations are accessible (probably start with Unova so you can just talk to Skyla after beating Unova Elite 4, and she can take you to the other regions), and where you can catch all the legendaries and Pokemon where they were originally able to be caught. Just a thought.