I want to see a Pirates team with Water and Dark Pokemon.
I also would like to see Team Rocket envolved in the next gen too.
I think it would be cool to see a new team and an old, resurrected team facing off and trying to conquer the world of Pokemon.
One team is helping you (Team A), the other isn't (Team B).
You do double battles with Team A throughout the game against Team B.
Team B is looking for the legendary opposite the one on the box.
Slowly throughout the game Team A gets obsessed with the legendary that is on the box.
Team A is stronger than Team B so they end up taking control of a legendary without getting foiled by you.
You have to fight the legendary, and use a special sort of Pokeball to capture it. (Something like a snag ball, so that you can cath a Pokemon during a battle)