Name: The Pokemon League
Basically, I want to see an enemy team that's already won. They Have the strongest pokemon, and they use them to extort, intimidate and blackmail shop owners, leaders of cities and families alike. Since they hold the strongest pokemon, they have taken the position of champion and the elite 4 alike. They have used those positions to corrupt the pokemon league into a recruitment system for them, gaining new members from those who earn badges.
The player would take the role of someone who defies the standing order, and joins in the fight to free the country, its people and its pokemon, from the oppression of these villains. He would seek (with the help of the underground) a legendary pokemon, whose power would allow him to defeat the "champion's" own legendary pokemon (which was which would obviously be switched depending on the version).
The rise to the top of the league would thus also represent to dismantling of the villains and the freeing of the relevant cities from the tyranny of the gym leaders, which would be represented in different items and features being available vs when they are still under the control of the League.
I think it'd be cool, at least.