I want something like R/S/E, but more like this:
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)