It could be a powerful Pokémon trainer. This trainer might see potential in Ash and decide to take him under their wing.
Perhaps a family living in a secluded Pokémon - rich area. They notice Ash's love for Pokémon and his determination, so they adopt him. They might have their own unique Pokémon that Ash gets to interact with and learn from.
Some of the gym leaders could also be involved. Maybe they feel threatened by Ash's new - found power as a champion. They might think that Ash will change the way the Pokemon battling world works and in order to stop that, they betray him. They could spread lies about Ash misusing his Pokemon or something similar.
One interesting aspect could be how Ash's relationships with different Pokémon change. Maybe he forms even deeper bonds with his starter Pokémon in this fanfic. For example, Pikachu might become even more protective of Ash.
Misty is a very likely candidate. She has been with Ash from the early days of his journey. They have a deep bond and have shared many adventures together. Their relationship has always had a bit of a romantic undertone, so in a fanfiction, it would make perfect sense for them to get married.
Perhaps an organization that believes dragon - type Pokemon are too dangerous and should be controlled. They see Ash as a threat because he is trying to master these powerful creatures. So, they constantly send their agents to stop Ash's progress in his dragon - master journey.
Definitely their close friends like Brock and Misty. They would be there to support Ash. And all of Serena's friends from Kalos too. Also, the Gym Leaders they've met along their journey might be invited. And of course, their Pokemon. Pikachu would be right there by Ash's side, and Serena's Fennekin would also be present.
A new, mysterious organization that is interested in controlling the legendary Pokémon. They see Latias as a key to their plan and Ash as an obstacle to be removed.
A powerful and greedy trainer who wants to capture Manaphy for its rare abilities could be the main antagonist. He might have a whole team of strong Pokemon and use underhanded tactics to try and get Manaphy.
It could also be a new character created specifically for the fanfic. Fanfic writers often introduce original characters to add new twists to the story. This new character could be someone who meets Ash during his travels and they gradually fall in love without the other main characters knowing.
It could be Team Rocket. Since they always cause trouble for Ash in the original series, in this fanfic, they might see Ash's transformation into a Pokémon as an opportunity to capture him and use him for their evil plans.
Team Rocket could always be the main antagonists. They might have a new and more devious plan to steal Ash's Pikachu and other rare Pokemon that Ash and Brock encounter on their journey.