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.
A powerful and greedy Pokemon trainer who wants to collect all the rarest Pokemon for himself could be the antagonist. He sees Ash's Pikachu and Brock's Onix as prime targets and will stop at nothing to get them. He could use underhanded tactics like setting traps for Ash and Brock during their travels.
A dark - type Pokemon that has gained an abnormal level of intelligence and wants to rule over all Pokemon. It sees Ash and Brock as threats to its plans because of their reputation for helping Pokemon. So it tries to eliminate them by sending out its minions to attack them at every turn.
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.
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.
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.
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.
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.
In this fanfiction, it could be a mysterious figure who has been secretly observing Ash and Brock all along. This figure might be from an ancient Pokemon - worshipping cult. They betray Ash and Brock because they see their presence as a threat to their long - held beliefs and practices regarding Pokemon. They might use underhanded tactics like stealing their Pokemon or spreading lies to turn the Pokemon community against them.
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.
For Ash, Pikachu is always a great choice as it's his most loyal and powerful partner. Alongside that, a strong flying type like Charizard could be useful. For Brock, his Onix would be a staple. And perhaps a water - type like Vaporeon could be good for him to balance his team. Since they are teaming up, having a psychic - type like Alakazam could also be beneficial as it can help in battles and also with communication in tricky situations.
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.