It could be Danzo. He might have some hidden motives and manipulate situations to make Naruto look like a threat, forcing Minato to arrest him.
Perhaps an unknown outsider who has infiltrated the village and planted false evidence against Naruto. This villain's goal could be to create chaos in Konoha by turning the villagers against Naruto and making Minato take such a drastic step.
It's possible that a rogue ninja from within the village, jealous of Naruto's growing power and influence, frames him. This ninja could be someone who has always been in the shadows and sees this as an opportunity to get rid of Naruto and undermine Minato's leadership.
Maybe there's some sort of misunderstanding or a powerful enemy who has framed Naruto. Minato, following the rules of the village, arrests Naruto. As Naruto is in prison, his friends try to find evidence to prove his innocence, and Minato gradually realizes he's made a mistake and starts to help them from the inside.
The Akatsuki could still be the main antagonists. However, in this fanfiction, they might target Naruto earlier because they know Minato is training him. They could fear that Naruto would become an even greater threat to their plans in the future. Pain, in particular, might see Naruto as a symbol of the Hidden Leaf's strength that needs to be eliminated. Also, there could be an internal antagonist within the Hidden Leaf, someone who is jealous of Naruto's special relationship with Minato and tries to undermine him.
Perhaps an ancient evil that was sealed away long ago is awakened when Minato is revived. This entity could be a powerful demon or a dark ninja from the past. It wants to destroy the ninja world and Minato stands in its way. Minato, with his skills and knowledge, has to figure out how to defeat this ancient evil with the help of Naruto and the other Leaf Village ninjas.
Perhaps a new and original antagonist could be created for this fanfiction. This antagonist could be a rogue ninja who has mastered a forbidden jutsu that allows him to manipulate time as well. He could be the one who sets up the events that lead to Minato's endangerment, and Naruto has to figure out his motives and stop him while also saving Minato.
Rin could also be an important character. She could be the one who takes care of baby Naruto's day - to - day needs, like feeding and cleaning. She could also have a special bond with Naruto, perhaps seeing him as a symbol of hope for the future of the village.
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.
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 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.