Here's an idea I like, but is HIGHLY unlikely to be put in...
Maybe there are two teams vying for control of the game legendary and you can decide
who you side with. like one is trying to wreak havoc, and the other is trying to save the world with it.
You still face gym leaders (for badges if you're good, and to eliminate obstacles if you're evil)
And instead of the elite four, you face four sub-leaders and main leader of the opposing team.
And yes, I hope beyond hope that they add light type... Doubt it though.
EDIT: I'm also in support of a more mean/evil rival. Or, if my idea comes to pass, on the opposing team.
And to modify my idea, the team you're on could be decided by the game you get.