In some cases, it could be a corrupted lost boy. Maybe one of the lost boys has turned bad due to jealousy or a desire for power. He sees the hurt girl as an easy target to assert his dominance or to gain something from her, like her friendship with Peter Pan. So he becomes the main source of trouble for the girl in the fanfiction.
One common plotline could be the girl facing emotional hurt from past traumas that are explored within the magical setting of Neverland. Maybe she was betrayed by someone she trusted in Neverland, like a lost boy who turned against her.
The mermaids could be the main antagonists. They are known to be jealous and territorial in the Peter Pan stories. If the lost girl catches Peter Pan's attention in a way they don't like, they could make her life in Neverland miserable. They might use their alluring voices and their knowledge of the waters around Neverland to try and drive her away or lead her into danger.
One idea could be exploring the backstories of the lost boys in more detail. Maybe one of them has a hidden connection to a character from the outside world. Another plot could involve a new villain coming to Neverland who has a different kind of magic that challenges Peter Pan. Also, a story about Wendy's granddaughter returning to Neverland to find a lost family heirloom could be interesting.
One underrated character is Felix. He's always by Peter Pan's side, but we don't really know much about his past or his motives. Fanfiction could explore his backstory, like maybe he was a lost boy who had a really tough life before coming to Neverland and that's why he's so loyal to Pan. Another could be the mermaids. They are often just seen as minor characters, but they could have their own complex society and relationships that could be delved into in fanfiction.
An original character could be an antagonist too. For instance, a powerful sorcerer who has been in hiding for ages but emerges because he senses the power of the Dark Swan. He could be jealous of her power and wants to steal it for himself. He might use his own brand of dark magic and his knowledge of ancient spells to try and defeat the Dark Swan and take over the magical realm.
Captain Hook would be a likely main antagonist. He has a long - standing feud with Peter Pan, so he would see Peter Pan's daughter as a target or a way to get revenge on Peter. He might try to capture her or use her to lure Peter Pan out of hiding if he's still alive in the fanfiction's version.
It could be a jealous rival. Maybe someone who was envious of Emma's skills or popularity. This person might have set a trap that led to Emma's injury, all in an attempt to get her out of the way so they could take her place in whatever it was she was good at, whether it was being a leader or having a special talent.
A powerful sorcerer could be the main antagonist. He might be jealous of Jack and May's emerging powers and see them as a threat to his own plans of ruling the land. So, he tries to stop them at every turn, creating various obstacles and sending his minions after them.
A young girl with the power to communicate with animals could be a main character. She might be the one who first discovers the strange happenings in the Golden Green and starts the journey to uncover its secrets.
She could be on an adventure to find a hidden treasure in an enchanted forest. Maybe she follows a mysterious map that she found in an old attic. Along the way, she meets talking animals that help her overcome obstacles.