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.
There could be a mad scientist - type character who created the situation where Ash turned into a Latias in the first place. But then, this character wants to keep Ash in that form to study him and use his new - found Pokemon abilities for their own gain. They would be the main obstacle for Ash in his journey to turn back into a human.
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 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.
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.
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.
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.
Maybe a powerful and evil pokemon trainer who has a vendetta against Ash. Now that Ash is in a vulnerable pokemon form, this trainer could try to capture and control him. The trainer might have some dark motives related to using Ash's unique situation to gain power in the pokemon world.