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Not exactly related, but I've always wanted this to happen in a Pokemon game:
In the beginning your region's professor implies he once was a trainer, but then gave up on it for certain reasons. He's the first trainer you fight and will use the starter weak against yours to give you an easier time. NPCs will mention that the region has no champion, since the last one stepped down and no one has beaten the E4 since. You'll get lines from him saying how he's impressed with you throughout the game, occasionally coming to help fight the evil team, even. After your eighth badge he'll be missing from his lab his aide will answer you instead and will just say he went somewhere. When you reach the E4 building they'll say the champion has finally returned, and you'll meet the professor at the end, talking about how seeing you has inspired him to live again.
His ace will be the starter weak to yours, who will have gained a second type that gives it an advantage as well.
