Maybe a new, powerful and evil Pokémon trainer. This trainer could be jealous of Ash's fame and skills, and when Ash becomes a Pokémon, this trainer wants to capture him and force him to fight in illegal Pokémon battles for profit.
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.
It could be a powerful and evil Pokemon trainer who wants to capture Ash in his new Pokemon form. This trainer might be after Ash because he believes that a human - turned - Pokemon has some special power or value.
It could be a trainer who hates Pikachu and wants to capture all of them. This would put Ash, as a Pikachu fan, in direct conflict with this trainer.
It could be a trainer who has a dislike for Charmander. This trainer might see Ash's new - found love for Charmander as a threat and try to undermine Ash's relationship with his Charmander. For example, this antagonist could try to steal Charmander or set up difficult battles where Charmander is at a disadvantage.
It could be a rogue Pokémon trainer who wants to capture Ash - now as Pikachu - for his own collection. This trainer might have a cruel streak and not care about the well - being of Pokémon.
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.
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.
It could be a powerful and jealous Galar trainer. This trainer might see Ash as a threat to their own reputation and success in the region. They would then use their influence and charm to turn Ash's friends against him.
Team Rocket could still be the main antagonists. They might see Ash as a Pikachu and try to capture him more than ever, thinking he's a special Pikachu. Maybe they believe he has some sort of new power because of his transformation.
Gary could be a main antagonist. He might be jealous of Ash's popularity at school and constantly try to undermine him in Pokemon battles and in front of their classmates.