A possible main antagonist could be a rogue scientist from Kim's world who has somehow gained knowledge of chakra and wants to use it to create an army of super - soldiers. He kidnaps some of Naruto's friends to study their chakra and it's up to Naruto and Kim to stop him.
A new character could be introduced as the main antagonist. Maybe a powerful alien who sees Kim's new powers as a threat to his plan of taking over the earth. This alien could have his own set of powers that are quite different from Kim's, like the ability to control minds. Kim would have to not only learn to use her new powers but also find a way to defeat an enemy with such a dangerous ability.
Shego could also be the main antagonist. Maybe she discovers a way to time travel on her own and decides to go back in time to eliminate Kim before she becomes a threat. Kim would have to follow her through time to prevent this and save her younger self.
It could be an evil scientist who wants to capture the cat girl for her unique abilities. Maybe he wants to use her enhanced senses or agility for his own malicious purposes.
The Organization in the Claymore world could be the main antagonist. They already have a lot of secrets and do some morally ambiguous things. If Naruto shows up and starts changing the status quo, like teaching Claymore warriors to be more independent, the Organization might see him as a threat and try to eliminate him.
It could be a rogue ninja who was once a student of Orochimaru and has now developed his own dangerous jutsu. He wants to take over the ninja world and believes the old ways are holding everyone back.
Orochimaru could be a great antagonist. He might want to use Shenron's power for his own dark experiments. He could try to steal the dragon balls and manipulate the wishes to gain immortality or create an army of powerful, immortal ninja.
It could be someone who opposes Naruto's newfound admiration for Ganondorf. Maybe a traditionalist ninja who thinks Naruto is straying from the true ninja path by getting influenced by Ganondorf.
Lex Luthor could be a great antagonist. He's always looking for power and knowledge. If he discovers Naruto's abilities, he might try to use them for his own gain or see Naruto as a threat to his plans in Smallville.
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.
A new character could be created as the antagonist. For example, an Uchiha who has been corrupted by the power of the Sharingan and wants to use Naruto's special Uchiha - related abilities for his own evil purposes. This character could be jealous of Naruto's unique position within the Uchiha - related story and try to take it from him.