Who could be the villain in a 'naruto and mei hypnosis fanfiction'?

Well, one possible plot could be that an enemy uses hypnosis on Mei and Naruto has to break the spell. He might have to go on a journey to find a rare antidote or learn a special jutsu to counter the hypnosis.

It could be a wandering sage. These sages are often full of strange and powerful knowledge. They might see potential in Naruto and decide to teach him hypnosis as a way to expand his combat skills.

Mojo Jojo is a likely villain. He's always trying to outwit the Powerpuff Girls, and hypnosis could be his new devious plan.

It could be Orochimaru. He's always interested in new forms of power and experimentation. He might see Wolverine as an interesting specimen to study and try to extract his healing factor or adamantium for his own purposes. This would put him in direct conflict with both Wolverine and Naruto, who would naturally oppose Orochimaru's evil plans.

It could be a new ice - using ninja who has a grudge against Naruto. Maybe this ninja wants to prove himself as the most powerful ice user and sees Naruto as a threat, so he freezes Naruto in ice.

Danzo could be a great main villain in a Naruto Frankenstein fanfiction. He's always been power - hungry and secretive. He might use the concept of creating a Frankenstein - like being to gain more power for Konoha in his own twisted way, but really it's all about his own control. He could be using parts of dead ninja's abilities or something like that, and Naruto would have to stop him.

Orochimaru could be a likely main villain. He has always been interested in Naruto's power and body. Maybe he finally devises a plan to kidnap Naruto and use his body for his own reincarnation experiments.

It could be Orochimaru. He might be interested in Ino's unique abilities, like her mind - control jutsu, for his own evil experiments. So he kidnaps her, and Naruto has to fight against Orochimaru's snake - like techniques to save Ino.

It could be Orochimaru. He might be interested in stealing the exosuit to enhance his own powers and immortality research. He could see the exosuit as a new way to achieve physical enhancements beyond what his current jutsu can do.

Another possibility is that the main villain could be a spirit or entity that has been trapped for centuries. It uses its influence to make the Hidden Leaf Village conduct 'experiment 101' on Naruto. The spirit hopes to use Naruto's body as a vessel to be reborn into the world and wreak havoc. So it manipulates the events and people involved in the experiment from the shadows.