A new villain could be introduced, a rogue ninja from a foreign land who has heard of the exosuit. This villain could be a technological genius in his own right and has created his own exosuit - like armor. He wants Naruto's exosuit to combine the two technologies and create an ultimate weapon to take over the ninja world.
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.
Danzo could also be a main villain in this scenario. He might view the exosuit as a threat to his control over Konoha. He would try to either take it for himself or destroy it to prevent Naruto from becoming too powerful and independent. Danzo is known for his underhanded tactics, so he could send root members to steal or sabotage the exosuit.
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.
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.
A new character could be created as the main villain. Maybe a rogue ANBU agent who was once a friend of Naruto and Sasuke but has been corrupted by power. This character would know all the ins and outs of the ANBU, making it very difficult for Naruto and Sasuke to stop him as he tries to take over the ninja villages using the secrets he learned while in the ANBU.
It could be Orochimaru. He has always had an interest in Konoha and its secrets. Maybe he decides to launch a full - scale invasion this time to get his hands on something he desires.
Perhaps a powerful ninja from another village who has a vendetta against Konoha and the ANBU. They see the ANBU's connection with Naruto as a threat and use their knowledge of the lemon fanfiction element in some way. For example, they might create clones that are disguised as lemon - scented ANBU members to infiltrate Konoha and cause chaos.
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.