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.
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.
A powerful demon lord from the underworld could be the main villain. This demon lord could be seeking to expand his territory into the Naruto world, using his dark magic and hordes of minions.
The main villain could be Kabuto. He's always been power - hungry. If he got hold of an Infinity Stone, he would use it to try and take over the ninja world. He could use the stone's power to enhance his own medical ninjutsu to the point where he could resurrect and control any dead ninja.
It could be a mad scientist - type ninja who creates the droid army. This ninja might be someone who was shunned by the ninja community for his unorthodox ideas about mixing technology and ninjutsu, and now wants revenge by using the droid army to take over.
Maybe Orochimaru could be involved with the League of Assassins and become the main villain. He has always been interested in power and dark arts, and the league could provide him with new resources and minions. He could use the league to target Naruto and try to steal his power or the Nine - Tails within him.
It could be an evil Digimon that has the power to control other Digimon and wants to use them to invade the Naruto world. This Digimon might be jealous of the Digimon King's power and Naruto's connection to it, so it aims to destroy both of them. It could have abilities like mind - control and dark energy attacks.
It could be Orochimaru. He's always been into strange experiments. He might create a robot army to get revenge on the village or to prove his superiority.