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.
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.
Maybe an ancient evil spirit that has been awakened due to some mistake. It targets Ageha because she has a pure and powerful chakra. Naruto, being the hero he is, tries to fight the spirit, but he quickly realizes that he needs Ageha's help as well as the help of all his friends to defeat this powerful foe.
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.
Orochimaru would make a great villain. He could be jealous of the new magical powers in the village and try to steal them for his own experiments. His snake-like abilities could be enhanced in a creepy way to contrast with the bright and shiny magical girl powers.
The main villain could be Darkseid. Imagine if he somehow finds a way to enter the Naruto universe. He would be a formidable foe for both Naruto and Supergirl. His omega beams and immense strength would be a huge challenge for them to overcome.
It could be a rogue ninja from the village with the Tenshikage. Maybe he's jealous of the Tenshikage's power and wants to take it for himself. He could be causing chaos in the village, stealing important ninja scrolls and attacking innocent villagers.
A new character could be introduced as the main villain. This character could be someone from an ancient clan that was once in control of the 10 - tailed beast but lost it. Now, seeing Naruto with that power, they want it back and will stop at nothing to get it. They could have unique powers and abilities that make them a formidable foe for Naruto and his friends.
It could be a new character, a powerful dark wizard who wants to use the combined power of Naruto's chakra and Pikachu's electricity for his own evil purposes. He creates all sorts of dark creatures and sends them after Naruto and Pikachu to try and capture them. He's very cunning and has a lot of minions to do his bidding.
A rogue ninja from a neighboring village could be the villain. This ninja might have a vendetta against Ino's family and uses Naruto as a tool to get to her. He hypnotizes Naruto because he knows Naruto is strong and his actions while hypnotized would create a lot of trouble for Ino and Konoha.