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.
Perhaps a Pokémon hunter who sees Pikachu as a valuable commodity. Since Ash has become a fan of Pikachu, he would oppose this hunter. The hunter might use underhanded tactics to try and catch Pikachu, which Ash would have to stop. Ash would need to use his knowledge of Pikachu and his other Pokémon to outwit the hunter.
There could be a new evil organization that believes Pikachu's power is a threat. They plan to eliminate all Pikachu. Ash, being a fan, would do everything in his power to protect Pikachu. He would have to team up with his friends and their Pokémon to fight against this organization. This organization might have powerful Pokémon of their own, making the fight a difficult one for Ash and his allies.
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.
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.
It could be a trainer who has a dislike for Charmander. This trainer might see Ash's new - found love for Charmander as a threat and try to undermine Ash's relationship with his Charmander. For example, this antagonist could try to steal Charmander or set up difficult battles where Charmander is at a disadvantage.
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 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.
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.
Well, perhaps Ash starts to idolize Pikachu after seeing its unique powers in a battle. He might try to imitate Pikachu's moves and even start collecting Pikachu - themed items.
Another possibility is a rival trainer who has a Pokemon that is weak against Raichu. This trainer might try to prevent Pikachu from evolving to keep their own Pokemon's advantage in battles. They could try to steal Pikachu's food or training resources to slow down its growth and evolution.
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.