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.
In this fanfiction, Lulu is likely a character who has the task of raising Naruto. She could be from a different realm or have a very different background from the Naruto universe. Maybe she's a sorceress or a wise woman with her own secrets and powers that she imparts to Naruto as he grows up.
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.
In this fanfiction, it could be that there is a prophecy that involves both Lulu and Naruto. The prophecy states that only by combining their powers can they save both their universes from a great evil. So, they meet and at first have communication problems due to their different backgrounds. However, as they train together and share their stories, they form a deep bond and work towards fulfilling the prophecy.