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 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.
Maybe the main antagonist is an evil scientist. The scientist has been studying Pokémon transformations and when he sees Ash turn into Pikachu, he wants to experiment on him. He chases Ash around, trying to capture him with all kinds of high - tech devices. This forces Ash to use his Pikachu form's abilities and his human knowledge to outwit the scientist.
Team Rocket could be the main antagonists. They might see Ash's transformation into Mew as a way to capture a powerful Pokémon - like being. They could devise all sorts of plans to catch him, thinking that they can use Mew - Ash's powers for their own evil purposes.
It could be a jealous trainer who doesn't like the attention that girl - Ash is getting. This trainer might try to undermine her at every turn during Pokemon battles.
Well, it could be about Ash somehow magically being transformed into a Latias. Maybe he then has to deal with the powers and instincts that come with being a Latias. He might try to find a way to turn back while also exploring the world from a new perspective as a Pokemon.
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.
Maybe Team Rocket could be the main antagonist. They might see Ash's transformation as an opportunity to finally capture Pikachu. Since Ash is in a more vulnerable state as a girl, they could try to use different tactics to take advantage of the situation.
Perhaps a jealous trainer. This trainer has always been envious of Ash's success and now that Ash is in a vulnerable state as a Zorua, the trainer sees an opportunity to get rid of him for good. The trainer could try to use his own Pokémon to capture Ash or even harm him, making the trainer a formidable antagonist in the story.
Maybe a powerful and envious Mewtwo could be the antagonist. Since Ash has now become a Mew, Mewtwo might feel threatened or think that Ash doesn't deserve such power. So, Mewtwo could try to fight Ash to prove his own superiority.
Perhaps a dark - type Pokémon that is jealous of Ash's new form. This Pokémon might see Ash as a threat and constantly try to attack him and stop him from getting used to his Latios form.