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 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 been interested in Sasuke and might target ANBU Team 7 to get to him. Orochimaru's experiments and his desire for power make him a formidable and menacing villain. He could also be using some new jutsu or have created more powerful minions to fight against Team 7.
Perhaps a powerful and unknown shinobi from a far - off land. This shinobi has heard of Team 7's reputation and sees them as a threat to his plans of world domination. He uses his unique and mysterious jutsu to challenge Team 7 at every turn, and they have to figure out his motives and weaknesses to stop him.
One option for the main antagonist could be a secret organization that has infiltrated Konoha. They target the Anbu prodigy because they fear the prodigy's abilities could expose their existence and plans. This organization might have members with unique and dangerous abilities themselves. They would constantly send assassins after the prodigy and try to create chaos in Konoha to keep the Anbu and the prodigy distracted while they carry out their real objectives.
It could be an evil shinobi who wants to capture the Kitsune Anbu for their unique powers. Maybe they want to use those powers to take over the Hidden Leaf Village. Another option is a rogue Anbu member who has turned against the village and sees the Kitsune Anbu as a threat to their own plans.
It could be a rogue ANBU member who has gone bad and is trying to expose Naruto's secret identity for some evil purpose.
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.