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Everyone in the Pokemon world goes on a journey at some point in their childhood. That's partly why so many people are willing to battle, they're either kids on their own journey, or they remember when they were kids going on their journey.
The not necessarily intended purpose of these journeys, but the product of them nonetheless, is to find what the individual is best at, and by extension what they will be able to contribute to the (relatively utopian) society.
Pokemon and humans work together to accomplish things for the benefit of all of society.
Every so often there will be a child prodigy who shows a great degree of competence, possibly genius, of Pokemon training and battling. These trainers will typically come to hold positions in the league, be it gym leaders, elite 4 or champion. The Player Characters are also examples of these prodigies.
Every so often, when a criminal team rises to power, the gym leaders and/or elite 4/champion will combat them.
However, when a criminal team rises to power around the same time a prodigy trainer is embarking on their journey, if the trainer takes it upon themselves to combat the team, the league will avoid involvement unless absolutely necessary (gym leaders at the end of B&W in Plasma Castle) so that the trainer may grow and develop.
