I thought about that and there's a lot of things to implement it into the storyline. There can be a strange person that he battled earlier in the game (before gym 2) and he recognizes his pure and loving heart (he's still a good person back then despite being bullied). After beating the 4th gym, he can give him the Silver Wing and the other item (I forgot right now) and tell him to go to a place to search for this strange legendary pokemon. He also gives him surf. This person can be the 8th Gym Leader or the Champion.
As for the age, I don;t think a 14 year old can rule a city, that's why I made him 16.
The league thing? Well just because it's pokemon doesn't mean you focus on beating gyms. You DO beat gyms so yeah
Okay, so basically it's this. He starts having evil thoughts after beating the 4th Gym and obtaining Lugia, which upsets it. Still, he gets to the 5th city, sees the bully again, stomps him with lugia and goes to the gym leader. The gym leader is an arrogant person, so before battle, he bragged about his son living in [YOUR HOMETOWN] and mentioned his name - [YOUR RIVAL]. Furious, you challenge him to battle for the gym badge and continue with your evil thoughts, claiming the town for your own.
After that, like I said, you need to rematch the previous gym leaders and claim the towns as well (by that, just replace people's clothes with the classic uniform of your team or make some changes here and there for mappers). I'm thinking of events during Gym 6 and an event during Gym 2.
Who's mapping? Oh and wait so that's the pokemon we can use in game? Nothing more? XD I WANT RIOLUUU.