It could be another powerful Pokemon trainer who wants to use Ghetsis and N's relationship for their own gain. Maybe they try to manipulate them into fighting each other so they can take over their influence in the Pokemon world.
A group of shadowy organizations that oppose the ideals of both Ghetsis and N could serve as the main antagonist. They see Ghetsis's past actions and N's unique connection with Pokemon as threats to their own power - hungry plans.
Perhaps a plot where Ghetsis and N are forced to team up against a common enemy that threatens the entire Pokemon world. As they work together, they gradually understand each other better and form a deeper bond.
It could be Orochimaru. He's always been interested in unique powers and abilities. The idea of X - 23's mutant abilities and Naruto's jinchuriki powers would be very appealing to him. He might try to capture them both to use in his experiments to gain ultimate power.
Maybe an evil sorcerer from a third, unknown dimension who sees the potential in both Naruto's chakra and Pneuma's power. He plans to steal their powers to become invincible. He starts by creating unrest in both their worlds, pitting their friends and allies against them. Naruto and Pneuma must figure out his true identity and stop him before he succeeds in his devious plan.
It could be an evil ninja who has somehow gained access to the technology from Neo's world and wants to use it to take over the Naruto world. He might be able to create clones using digital technology, making him a very difficult enemy to defeat.
A new, mysterious organization that wants to control the chakra of strong ninja could be the main antagonist. They see Inojin and Himawari as prime targets due to their unique abilities. The organization would try to capture them, which would force Inojin and Himawari to fight together and also test their relationship as they face this powerful threat.
An old rival of Dino's from his past could show up. This person might have a grudge against Dino and decides to target Hibari as a way to get to Dino. Since Hibari is so proud and strong - willed, he doesn't take kindly to being used as a pawn, and together with Dino, they have to face this old enemy. This antagonist could have some powerful fighting abilities or some dark secrets that make it difficult for Dino and Hibari to defeat him.
Dr. Eggman could be a great antagonist. He might be creating a new weapon or device that could disrupt the balance between time (which is relevant to Silver) and space (relevant to Shadow). His actions force Silver and Shadow to work together to stop him.
An ancient evil entity that has awakened and sees Ulbert and Demiurge as a threat to its domination. This entity could have powers that are difficult for them to counter, and it uses psychological warfare as well as physical attacks. For instance, it might try to corrupt Demiurge's loyalty or make Ulbert doubt his own abilities.
Vilgax could be a great main antagonist. He has a long - standing feud with Ben and his appearance would immediately up the stakes. He could also manipulate Kevin into turning against Ben for a while.
It could be a character who wants to disrupt Newton's laws in the world where Sackboy has landed. Maybe a mad scientist type who believes that chaos is better than the order imposed by Newton's principles. This antagonist could create all sorts of dangerous situations for Sackboy by messing with the normal gravitational and physical forces.