Sakura Haruno from an 'evil - turned' alternate universe. Imagine if something had gone terribly wrong in her life that made her turn against Konoha. She would already have a connection to Naruto from the original storyline, which could add depth to their interactions in the fanfiction. Naruto would be conflicted because he knows the 'good' Sakura, but now has to deal with this new, villainous version.
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.
Konan could also work well. She was once part of Akatsuki, an organization full of villains. Although she had her own reasons for her actions, she was still on the wrong side from Konoha's perspective. Naruto could encounter her during a mission and their relationship could develop from there. Maybe Naruto tries to understand her pain that led her to be part of Akatsuki and in the process, they form a bond.
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.
A new villain could be created specifically for this fanfiction. This villain could be a being that feeds on the chaos between the two different universes. It has the ability to disrupt chakra flow in Naruto's world and nullify magic in Lulu's world. Naruto and Lulu would have to figure out how to work together to stop this entity before it destroys both of their homes.
It could be a rogue shinobi who has found a way to enter the Matrix world and wants to take over both the real world and the Matrix. He uses his ninja techniques combined with the power of the Machines to create havoc.
Kabuto could also be a main villain in this context. He might see the potential in the gloves to further his own power - hungry goals. He could try to manipulate Naruto into using the gloves in a way that benefits him, or he could simply try to steal the gloves when Naruto is at his weakest.
It could be an evil ninja who has somehow gained access to Gem technology. He uses the power of the Gems to enhance his own jutsu and becomes extremely powerful. His goal could be to take over both the Naruto world and the world of the Gems.
Perhaps an evil organization that wants to capture Ino for her unique mind - related abilities. They believe they can use her powers for their own malicious purposes. Naruto and the rest of the team then have to protect Ino and take on this organization. The leader of this group could be the main villain, with his own set of powerful and dark jutsu.
It could be Orochimaru. He might be interested in Tenten's unique weapon skills and Naruto's power of the Nine - Tails. He could try to capture them to conduct experiments on how to combine their powers for his own gain. He might create some sort of hybrid - clone with Tenten's weapon - using abilities and Naruto's chakra.
Madara Uchiha could also be a main villain in this crossover. He could be interested in the power of the Triforce in the Zelda world. He might try to manipulate Link and Zelda to get to it. His Sharingan abilities would make him a formidable opponent in the world of Zelda, and his large - scale plans could involve taking over both the Naruto and Zelda universes.
A powerful dark wizard from the mysterious kingdom could be the main villain. He might be jealous of Naruto's powers and see him as a threat to his rule over the kingdom.
The yandere female villain can be characterized by her extreme possessiveness. In the DC context, she might be jealous of any other character who gets close to the OC. For example, if the OC is friends with Batman, she would try to sabotage that relationship. She could also have a volatile temper, going from sweet and loving towards the OC one moment to enraged and violent the next if she feels the OC is slipping away.