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.
One idea could be that the female villain initially tries to use Naruto to further her evil plans but ends up falling in love with him. For example, she might pretend to befriend him to get closer to some powerful jutsu he has access to. But as she spends time with Naruto, she sees his unwavering determination and kindness, which starts to change her perspective. Another plot could be that Naruto has to team up with the female villain against a greater threat. During their time together, they have to overcome their differences and learn to trust each other.
It could be a combined villain. For example, Orochimaru from the Naruto universe teams up with a powerful magic - user from Wanda's world who is jealous of Wanda's powers. This villain duo could be really menacing as they combine Orochimaru's dark jutsu and the magic - user's powerful spells.
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.
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.
She could be a hero. In fanfiction, a female Naruto might use her determination and unique skills to protect the village. Just like Naruto in the original, she could have a strong will to overcome any obstacle and befriend those who were once enemies. For example, she might form a bond with Sasuke-like characters in a different way, using her charm and understanding to prevent him from going to the dark side.
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.