If Ash ends his adventure as a world champion and still has to star in anime, it would be nice to continue as the main character but play the role of the villain. Preparing a plan to exterminate half of humanity to justify the punishment for people who do not trust pokemons after the event of a successful theft of his Pikachu and over 80 pokemons by Team Rocket with Giovanni's supervision.
So that's what I thought about it, and why not add such a dark story just like as it was with Lysandre, but with long story? So I will write like this:
Ash looking for more powerful legendary pokemons, establishing friendships with them, understanding each other and sharing the same opinion about people who treat pokemons cruelly. His second goal would be to retrieve his old pokemon and catch some new pokemon.
Hiding behind being a villain under a good person, he decides to pretend to be the mentor of a certain new trainer. So everyone, not even his former companions, cannot suspect him of insane, sinister plans - stealing important equipment in the laboratory, kidnapping several professors, gaining information from them through torture by his new pokemons, orders of pokemon attack on people instead of their pokemon, even later on former companions. All these crimes are made to change the world into beauty without cruel people unloving their pokemons. Ash is characteristically worried about pokemons than humans, which is why the legendary pokemon consider him worthy of being a trusted person.
After the success of Team Rocket, Ash's personality loses joy, happiness, full of energy. Instead, he becomes depressed, becomes aggressive towards loved ones, and no longer trusts anyone except his mother. Only Pikachu returning to him can bring joy, happiness back to Ash.
Ash succeeds in devastating half of the people on Earth and the Pokémon trust him even more, they restore happiness to all Pokémon.
Then Celebi is the perfect fit here to change Ash's past, and so will the new protagonist (that new trainer) from this arc of the story (Celebi Arc).
Everyone is fighting for Celebi about the desire to change the world. After Celebi intervenes, Ash and the new protagonist will land in the past looking for where Pikachu might have ended up. It turns out that it ended up in new villain team headquarters, in the Pokemon Experiment department. So Celebi brought them to the future they came from here - Ash got a new hope, a new goal, find all his old Pokemon and mend his friendship with his former companions and apologize to them for his cruel deeds. The final episodes would be the final duel between Ash and the new protagonist with a full team of legendary Pokemon.
New trainer - I would suggest this to Bonnie as a new trainer 5 years later after focusing on the official Ash and Pikachu adventure. Ash would be 15 years old. Bonnie is strongly oriented towards pokemon, in the design Yellow from Adventures Manga would fit her profile very much and she would have to get her own Pikachu (that's why Ash chose her as his apprentice). She is very excited about adventures with pokemon, fighting gym leaders, fighting in the pokemon league and then the world championship to defeat her old companion and mentor.
I would like to see this:
Ash team:
- Gengar
- Incineroar
- Greninja
- Gardevoir (new, mega-evolution, new ace of team)
- new pokemon from new gen
- second new pokemon from new gen
Ash final team:
- Mewtwo (ace of team)
- Giratina
- Arceus
- Eternatus
- Necrozma
- new legendary pokemon from new gen
Bonnie's team:
- Pikachu (ace of team, make sense cause Ash is her mentor)
- Dedenne
- Braixen (get from prof. Sycamore)
- new pokemon from new gen
- new pokemon from new gen
- new pokemon from new gen
Bonnie's final team:
- Moltres
- Zapdos
- Articuno
- Xerneas
- Yveltal
- Zygarde (ace of team)
Well, I can only dream like this because anyway the writers would rather not take them to my idea. But that would be more interesting, wouldn't it? It would be fun to create a manga with this story just like doujinshi. Besides, forgive my awful syntax of sentences.