Another possible main villain could be a new character created specifically for the fanfiction. This character could be an ancient ninja who was sealed away long ago but is released when an Infinity Stone is unearthed. He wants to use the power of the stone to take revenge on the modern - day ninja clans for sealing him away in the first place.
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.
One possible plot could be that Naruto discovers an Infinity Stone during one of his missions. Maybe it was hidden in an ancient ruin. This stone gives him new powers, like the ability to control time briefly. With this new power, he tries to prevent some of the past tragedies in the ninja world, such as the Uchiha massacre.
Darkseid would be a great main villain. He's already a powerful and well - known foe in the DC universe. He could be the one who starts collecting the Infinity Stones - like items to gain ultimate power and rule over all universes. His army could also be involved, making it a large - scale war for the Justice League.
A likely main villain could be Kronos. He's always been after power and the Infinity Gauntlet would be the ultimate tool for him to finally overthrow the Olympians and rule over everything. He could sense the power of the gauntlet and do whatever it takes to get his hands on it.
Well, it could still be Thanos. His goal of collecting the Infinity Stones would be a great threat to Superman's world as well. Superman would have to figure out how to stop Thanos from using the stones' power on a galactic scale.
Madara Uchiha could be a great antagonist. He already has powerful jutsu and a thirst for power. If he gets wind of the Infinity Gauntlet, he would surely try to take it for himself to achieve his goal of creating a world under his control.
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.