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.
It could also be a new villain created specifically for this fanfiction. Maybe a powerful being that is a result of the mixing of chakra and the magic of the Zelda world. This villain could have unique powers that neither Naruto nor Link have faced before and would force them to work together in new and unexpected ways.
Death itself could be the main antagonist. It could be a force that doesn't have a physical form at first but starts to possess characters or objects in the Zelda universe. For example, it could possess Ganon, making him even more powerful and malevolent. Or it could be an unseen presence that is slowly draining the life out of Hyrule, causing plants to wither and people to fall ill.
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.
One option for the main character is an OC (original character) who has the spirit of Naruto inside him but looks like Link. He has the determination of Naruto and the adventuring skills of Link. In the harem, we could have Ino from Naruto. She's confident and has her mind - related jutsus. And from Zelda, Midna could be a part of it. She is a complex and powerful character. Another character could be Hinata. Her shy yet strong nature would add an interesting dynamic to the harem.
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.
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.
Another possibility is that it could be Zelda herself. She is a powerful character with magic abilities. She could be the main character trying to use her powers to stop the Keeper of Darkness from plunging Hyrule into eternal darkness.