A former ally of Ben or Rex who has been corrupted by the power of both the Omnitrix and the nanites. This character would know all their weaknesses and strengths, and would use that knowledge against them. They would be very conflicted, which would make them a complex and interesting villain. There could be moments where Ben and Rex try to reason with them, but the corrupted ally is too far gone in their pursuit of power.
I think an evil scientist who has found a way to combine the power of the Omnitrix and the nanites in a wrong way could be really interesting. He could be creating hybrid monsters that are very difficult for Ben and Rex to defeat. He would be constantly one step ahead because he understands both technologies so well.
A powerful interdimensional being that can manipulate the very fabric of the Omnitrix and Rex's nanites. This villain could be using their powers for its own amusement, creating chaos in both Ben's and Rex's worlds. It would be a formidable foe as it doesn't have a physical form that can be easily defeated, and Ben and Rex would have to find a way to either trap it or change its nature. This would force them to think outside the box and explore new ways of using their powers.
It could be Ben when he transforms into Alien X. Alien X has near - omnipotent powers. He can manipulate reality on a cosmic scale. In a crossover, he could potentially use those powers to control the Nanites or even restructure Rex's powers in some way. However, he's also very difficult to control, so it's a double - edged sword.
Another plot could be that an interdimensional rift opens up, and it's causing chaos in both Ben's and Rex's worlds. They discover that the source of the rift is related to the technology of both the Omnitrix and the Nanites. Together, they journey through the rift to find the cause and close it. Along the way, they meet alternate versions of themselves and their friends, which adds an interesting twist to the story.
One idea could be that Ben and Rex have to team up to stop a new villain who has the ability to disrupt both Omnitrix - based powers and Rex's nanites. They start off not trusting each other but as they face challenges, they learn to work together.
In a fanfiction crossover, they could end up in each other's universes by accident. Ben finds himself in a world full of EVOs and has to rely on Rex to get back home. Meanwhile, Rex is intrigued by the Omnitrix and tries to figure out how it works. They face many challenges together, like dealing with Rex's old enemies who see Ben as a new target.
At first, they could be rivals. Ben might think Rex's nanites are too unpredictable, and Rex could see Ben as a bit of a show - off with his Omnitrix. But as they face common enemies, they start to respect each other. For example, when they're both captured by a powerful villain, they see how the other fights and starts to understand their strengths.
One interesting crossover could be their powers combining in a unique way. For example, Ben could use one of his alien forms' abilities in tandem with Rex's nanites. Maybe Heatblast's heat powers could supercharge Rex's nanite - based weapons. Another aspect could be their personalities clashing and then learning from each other. Ben, being more of a carefree hero at times, could teach Rex to loosen up a bit, while Rex's more serious and scientific approach could help Ben be more strategic in his battles.
There could be a plotline where an ancient artifact is discovered that has the potential to either destroy or save both the world of Ben 10 and Generator Rex. Ben and Rex are drawn to it for different reasons. Ben thinks it could be a powerful weapon against his enemies, while Rex believes it could help him understand more about the origin of nanites. However, they soon find out that there are many forces trying to get their hands on this artifact too. They must protect it from falling into the wrong hands and also decide what to do with it in the end. This would involve a lot of action, adventure, and moral dilemmas for both characters.
It could be Ben himself. Imagine him using his alien forms in the Naruto universe. His Heatblast form could be really useful against ice - based jutsu, and Four Arms could take on some of the physically strong ninja. He would bring a whole new element of power and chaos to the Naruto world, and his reactions to the different cultures and powers in Naruto's world would be interesting to explore.
Definitely include Six. He's Rex's mentor and his combat skills and knowledge would be valuable in any crossover. If it's a crossover with a superhero team, he could offer strategic advice.
One idea could be a crossover with Ben 10. Rex's nanites and Ben's Omnitrix could lead to some interesting power clashes and team - ups. They could face a common enemy that requires both their unique abilities to defeat. For example, an alien - nanite hybrid villain.