Captain Hook would be an obvious choice as the main villain. He already has a long - standing feud with Peter Pan in the original story. In a Kingdom Hearts fanfiction, he could team up with the Heartless or be influenced by the Darkness to become even more menacing. He could also be after the power of the Keyblade, thinking it would give him an edge over Peter and his friends.
The Shadow, which is a manifestation of the Darkness in Neverland, could be the main villain. It could grow stronger and start to possess the other inhabitants of Neverland, turning them against Peter Pan. It could also corrupt the dreams that fuel Neverland, making it a darker and more dangerous place. Sora and Peter would have to work together to find a way to purify the Shadow and restore the balance in Neverland.
You could write a fanfiction where Peter Pan decides to leave Neverland and join Sora on his journey through the different worlds in Kingdom Hearts. This would bring a whole new dynamic to the group. Peter's carefree and adventurous nature might clash with some of the more serious characters, but at the same time, his skills and knowledge of magic could be a great asset. He could also introduce Sora and the others to new areas in Neverland that they haven't explored yet, which might hold secrets related to the Heartless or the overall plot of Kingdom Hearts.
It could be a group of outcast Lost Boys who have turned bad. They might be jealous of Wendy's special place in Peter's heart and in the group. So they kidnap her in an attempt to show Peter that they are in control now and can disrupt the harmony of the group.
Captain Hook could be the main villain. He might see the Little Mermaid as a new target or a way to get to Peter Pan. He could try to capture her and use her as bait to lure Peter Pan into a trap.
A possible main antagonist could be a corrupted version of Bellwether. After her time in prison, she could find a way to tap into the power of darkness. She wants revenge on Zootopia and uses the Heartless to cause chaos. She would be a devious antagonist as she already knows the ins and outs of Zootopia.
Sora would be an obvious choice as he has been the central character throughout the series. His journey doesn't end with the defeat of Xehanort, and there are still many things he could experience in the aftermath.
Sora would definitely be a main character. He's the protagonist in the Kingdom Hearts series, so it makes sense for him to be involved. The dalmatians themselves, especially Pongo and Perdita, could also be main characters. They could lead Sora through their world and help him understand their unique situation.
It could also be a new character, perhaps a dark sorcerer who is jealous of the magic in Neverland. This sorcerer might target Emma because she has an unknown power within her that could disrupt his own plans for the magical world. He would try to separate her from Peter Pan and use her power for his own evil deeds.
Captain Hook would be an obvious choice. His hatred for Peter Pan could extend to Moira when she becomes Peter's friend. He might see her as another obstacle in his quest to get revenge on Peter.
It could also be a new character created specifically for the fanfiction. This character could be from the world of the crossover and have some special ability or knowledge that helps in the fight against the Heartless. Maybe they have a deep understanding of the magic or technology in their world that can be used to counter the Heartless threat.
Perhaps an older, forgotten enemy of the Lost Boys could resurface. Maybe someone from their past in Neverland who they thought was defeated but has now returned with a vengeance. This could be a character who was once a Lost Boy himself but turned bad due to some dark influence in Neverland.