Quoted By:
>Why the hell do evil organizations still exist in fiction when the leaders know they're going to get defeated eventually? Mostly by some punk ass hippie kid and his friends? Or something else in that matter?
FTFY. This problem is not unique to Pokemon. This is common to virtually all fiction that has defined heroes and villains.
The ideal solution would be to completely remove the idea of a plot, make all options for success (Gyms/League, Pokedex, Contests/Pokeathlon/whatever, Medals/achievements) equally valid for "completing" the game, or not have an ending at all and just let the player wander around and do random bullshit.