A new character could be introduced as the antagonist. For example, a mad scientist who is interested in Ash's transformation and wants to study him. This scientist could try to capture Ash and keep him in a lab to run experiments on him, which would be a big threat to Ash and his friends.
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 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.
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.
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 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 group of Team Rocket - like villains could be the main antagonists. They might want to capture Pikachu while it's in the process of evolving because they believe that an evolving Pikachu would have some special power that they could use for their evil plans. They constantly try to disrupt Pikachu's evolution and the bond between Pikachu and its trainer.
It could be a jealous trainer. This trainer might see Ash in his shiny pokemon form and want that power for himself. So he tries to capture Ash by any means necessary, setting up all kinds of traps and challenges for Ash and his friends.
A jealous male trainer could be the main antagonist. He might see Ash's transformation as an unfair advantage given by some mysterious power. He constantly tries to undermine her in battles and challenges, believing that a female should not be as successful as a male in the Pokemon world.
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.