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 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 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.
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.
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.
An ancient and powerful Pokémon with the ability to influence Pikachu's mind could be the antagonist. It might see Pikachu's potential and wants to use it for its own dark purposes. By making Pikachu leave Ash, it can start to manipulate Pikachu more easily.
Team Rocket could still be the main antagonists. They might see Ash as Pikachu and think it's a new, rare Pikachu. So they try to capture him more desperately than ever. They could have some new gadgets designed specifically to catch this 'strange' Pikachu which is actually Ash.
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.
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.