The Phantom Troupe could be antagonists. They are a group of dangerous criminals in the Hunter x Hunter world, and they might see Kaito as a threat or a target for their own purposes. Another potential antagonist could be some of the more corrupt members of the Hunter Association who might not like Kaito's independent ways. There's also the possibility of new, original antagonists created specifically for the fanfiction, like a powerful dark magician who wants to use Kaito's power for his own evil plans.
A possible plot for 'Kaito Hunter x Hunter fanfiction' is that Kaito enters a special tournament in the Hunter x Hunter world. This tournament has rules and challenges that are different from the normal ones. He meets new and interesting characters during the tournament, some of whom become his friends and some his enemies. As he progresses through the tournament, he uncovers a conspiracy that is related to the very foundation of the Hunter x Hunter world. He then has to decide whether to expose it and risk his life or keep quiet and let the conspiracy continue.
For Miku, she could be kind - hearted, just like the Cinderella we know. She might be shy at first but has a strong will inside. She is creative, maybe shown through her music or art. Kaito could be brave, like Romeo, not afraid to pursue Miku despite the potential difficulties. He is also charming and confident, which makes him attractive to Miku.
You could try looking on Archive of Our Own (AO3). There are often many well - written Vocaloid fanfics there. Just search for 'Kaito x Gakupo' and you'll likely find some interesting ones.
A 'shinichi kudo x kaito kid fanfic' often explores the interesting dynamic between these two iconic characters. It could involve their rivalry turned into an unlikely friendship or a team - up against a common enemy. Writers might play with their different skillsets, Shinichi's detective abilities and Kaito Kid's thieving skills with a touch of magic.
To develop the female Kaito, focus on her relationships. She could have a mentor - like relationship with an older female thief who teaches her the ropes. In terms of her skills, she might be more attuned to using technology in her heists compared to the male Kaito. Also, explore her motives. Is it for the thrill, for justice, or something else? Her emotional journey as she becomes more and more like a great thief is also important to develop.
The Hunter x Hunter manga is unfortunately not complete. The author has faced various issues that have led to intermittent breaks and an unresolved storyline.