Maybe a power - hungry scientist. He has been studying the symbiotes and when he sees that the boy has a connection with one, he becomes jealous and wants to separate them so he can study the symbiote on his own and use its powers for his unethical experiments.
It could be another symbiote - a corrupted one that wants to take over the boy's symbiote for its own power gain. This corrupted symbiote might be controlled by an evil organization that is trying to use symbiotic powers to rule the world.
There could be a group of super - villains in the city who see the boy and the symbiote as a threat to their criminal activities. They team up to try and defeat the boy and the symbiote, constantly devising new plans to undermine them and take over the city.
In this fanfiction, the main antagonist could be a strict teacher. Sakura, being a boy with a free - spirited nature, often clashes with the teacher's rigid rules. The teacher always seems to be out to get Sakura, giving him unfair punishments and trying to suppress his creativity or individuality.
A powerful and corrupt Pokemon trainer could be the antagonist. This trainer is jealous of the boy's unique transformation into a Pokemon. He wants to use the boy's powers for his own gain, like winning all the Pokemon battles and championships. So, he hunts the boy down, causing all sorts of trouble for him during his journey as a Pokemon.
A powerful wizard who is conducting some strange experiments. He thinks that by forcing a boy to be a princess, he can create some sort of magical balance in the world. He doesn't care about the boy's feelings or rights and just uses his magic to enforce this transformation.
One possible plot could be that the boy discovers the symbiote in a mysterious place, like an abandoned laboratory. The symbiote initially scares the boy but then they gradually form a bond as the symbiote helps the boy protect his family from some local bullies who have turned into a more dangerous threat with the help of a strange artifact.
It could be Captain Hook. Since Harry Potter has magic, Hook might see him as a huge threat to his plans in Neverland. He would try to capture Harry and use his magic for his own evil purposes, or simply get rid of him to maintain his control over the island.
Perhaps an evil organization similar to the Akatsuki. They hear about the unique abilities of the little boy and decide that he would be a valuable asset to their plans. Their leader could be a mysterious figure with a vendetta against the Hidden Leaf Village and sees the boy as a way to get revenge.
Trigon could also be the main antagonist. Given his immense power and his connection to Raven, he could target Beast Boy as a way to get to Raven or simply to cause chaos among the Teen Titans. His demonic powers could be too much for Beast Boy to handle, ultimately resulting in Beast Boy's death.
It could be someone from the Naruto universe who doesn't like Naruto's newfound fascination with Aku. For example, Danzo might see Naruto's interest in Aku as a threat to the stability of the village and try to stop Naruto from further exploring Aku - related things. So, Danzo could be the main antagonist in this case.
It could be a new character, like a bully at school who doesn't like Ron's new bad boy attitude and constantly tries to pick fights with him.
Perhaps a mysterious figure from the outside world, like an evil sorcerer who discovers the magic that was used on the Nimh animals. He could see it as a way to gain power for himself and decides to capture the animals and drain their intelligence or magic. This sorcerer would be a formidable antagonist as he has powers that the animals have never faced before. He could also send his minions, like dark spirits or enchanted animals, to harass and attack the Nimh colony. Another possibility is a jealous rival from another intelligent animal colony. They see the success of the Nimh colony and want to undermine it, so they start spreading false rumors and causing internal strife among the Nimh animals.