My proposal is as follows: Once you have finished the history of all available regions and after you have defeated the villain team of your respective region, you could open a special location where there is a mini story about what happened to the evil teams and because they are there. You would enter the dungeon of the villain team of your choice (such as the election of the member of the Elite 4 in Unova) and you would have to fight against several recruits until you find the final boss, who would have in his Team some legendary of their respective region. You could do it with between 2 people in link and the serious reward: PB, money, RP. The pokemon with whom you accepted the challenge would have a ready or could have some exclusive particle.
Personally I think this proposal would be fine if they are trying to make their own dungeons and make it a good Postgame for those who love the history of the main games.