Another plot idea is to have a story centered around a Pokemon that has been misjudged in the Indigo League. Maybe it's a dark - type Pokemon that everyone assumes is evil. But the main character, a trainer, sees its potential and trains it to become a champion - level Pokemon. The trainer has to overcome the stigma associated with the Pokemon type and prove that it can be just as strong and noble as any other Pokemon.
One idea could be a trainer with an underdog Pokémon that has a unique ability not fully understood yet. They face many challenges in the Kalos League but gradually learn to harness that ability to surprise opponents. For example, a trainer with a Skitty that has a hidden psychic ability.
One idea could be a new trainer who has an unusual Pokemon partner, like a shiny Pokemon with a unique ability, and they enter the Champions League. Their journey through the league is filled with unexpected battles and they have to learn new strategies on the fly.
One idea could be a story about an underdog trainer who enters the Master League with a team of rare but not-so -popular Pokemon. They face all kinds of challenges and discrimination from other trainers who have more common and 'powerful' Pokemon. But through their unique bond with their team, they start to surprise everyone and make it far in the league.
One idea could be a trainer from a small, unknown town who enters the Pokemon Champion League with an underdog team of Pokemon. Another could be a story about a former champion who comes back to reclaim their title after a long hiatus. Maybe a story where a trainer has to face unexpected challenges during the league, like a new type of Pokemon or a rule change.
One interesting plot point could be how Ash overcomes his toughest opponents in new and unexpected ways. Maybe he develops a unique battle strategy that catches everyone off - guard.
Ash could encounter a legendary Pokemon in the Unova League that decides to help him in his battles. This would be a huge advantage and also a great plot twist.
Ash Ketchum is an obvious choice. He's the main character in the original series and has a lot of room for different storylines in fanfiction. You can explore his journey in the Indigo League from different perspectives, like what if he had made different choices during battles.
One idea could be the main character being reborn as a Pikachu and having to navigate the world with its electric powers while making friends with other pokemon. Another could be being reborn as a Eevee and having the unique ability to evolve into any form at will, which causes both envy and admiration among other pokemon. Maybe the reborn pokemon has memories of being a human and uses that knowledge to outwit trainers and other threats.
One possible plot could be that the Pokemon and Justice League members have to team up to stop an evil force that is trying to take over both the Pokemon world and the cities protected by the Justice League. Maybe a powerful, shadowy villain has discovered a way to use Pokemon powers in the human world in a very destructive way, and only by combining the unique abilities of the Pokemon and the superpowers of the Justice League can they hope to defeat this new threat.
One idea could be a story where the characters from Naruto are transported to a different dimension within the League of Shadows' realm and have to fight new and unknown enemies. They could form unexpected alliances with some of the League of Shadows' members who have a change of heart.