I think Orochimaru could also fit the bill. His experiments on himself and others are really out there. He's constantly looking for ways to gain more power and immortality in some really strange and unethical ways. His snake - like features and his ability to shed his skin like a snake add to his quirkiness. He's not your typical, straightforward villain and has a lot of idiosyncrasies that could be played up in a fanfiction.
Maybe Kabuto. He started out as a rather unassuming character but then became more complex and villainous. His ability to mimic the powers of others is quite unique. He could be made into a really quirky villain in the fanfiction by having him use these powers in unexpected and comical ways, like accidentally mimicking the wrong power at the wrong time or using a really powerful but also really silly - looking technique.
In this 'naruto the quirky villain fanfiction', the villain could be a master of illusions but in a very unorthodox way. Instead of creating fearsome or menacing illusions, they create really absurd ones like a world filled with giant rubber ducks. The villain could also be a talking animal that has somehow gained ninja powers and uses them in the most unpredictable ways. They might befriend some of the minor characters in Naruto and use them for their own comical and mischievous plans.
Kaguya could be an interesting choice. She is extremely powerful and has a complex backstory. Her motives were initially self - serving and evil. If she were somehow resurrected or a situation where Naruto had to interact with her in a different time - line, it could make for a great fanfiction. Naruto's ideology of peace and friendship could clash and then potentially influence her.
A powerful and corrupted sage could be the villain. He has delved too deep into forbidden arts and mastered hypnosis among other dark techniques. He views Naruto as a potential obstacle to his goal of spreading chaos and Mei as a valuable asset to be controlled. He uses hypnosis to try and manipulate them into doing his bidding. This sage could have a backstory of being shunned by the ninja world for his unethical practices, which has led him to seek revenge and power through any means necessary, including using hypnosis on Naruto and Mei.
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.
It could be a new ice - using ninja who has a grudge against Naruto. Maybe this ninja wants to prove himself as the most powerful ice user and sees Naruto as a threat, so he freezes Naruto in ice.
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 Ino's unique abilities, like her mind - control jutsu, for his own evil experiments. So he kidnaps her, and Naruto has to fight against Orochimaru's snake - like techniques to save Ino.
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.