blue notwithstanding. think about it:
>champion just means you're strongest in the region, doesn't necessarily mean you're respected
>9 times out of 10 if some kind mysterious individual helps you out in the main story they're the champion, big surprise
>pokemon always has themes of hard work & friendship over innate talent or seeing pokemon as tools to win with
>champion is supposed to be the end of the main game
so why not have a champion who's a super arrogant fuckface and only sees his team as tools for victory? it'd be a battle you actually want to win not just to become champion, but because his ideals directly conflict with the core values of pokemon