I do have some questions, do you have any plans to have Pokemon that evolve by trading, and how will they evolve ie. regular way, level, leveling up with item?
And if you want an idea for what the villians want they could want to take over the region and then the world, use some legendary psychic Pokemon to control the people of the region to do their bidding, gym leaders, rivals, and maybe even the Elite Four, as the player will have to stop this attempt and eventual success of this plan, but just a thought.