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.
Another option is a new, mysterious character who has a connection to an ancient evil. This character sees Sayuri Uchiha as a key to unlocking some dark power and Naruto as the one who will try to stop it. So, this character tries to either manipulate Sayuri or get rid of Naruto to achieve their evil goals.
The Akatsuki could still be the main antagonists. Since Naruto now has Uchiha powers, they might be even more interested in him. They could see him as a threat or a valuable asset to their plans, just like they did with Sasuke.
It could also be a member of the village leadership who has a deep - seated prejudice against the Uchiha. This person is constantly trying to undermine the Uchiha's position and is willing to start and fuel the wars in order to get rid of them. They see the Uchiha as a threat to the stability of the village.
I think Naruto and Itachi could also be main characters in this fanfic. Naruto might look up to Itachi for his self - sacrifice and powerful abilities. Itachi could act as a mentor - like figure to Naruto in the context of the fanfic, guiding him in understanding the Uchiha clan better.
Sasuke Uchiha could be a great choice as the main character. He already has a complex backstory and a lot of room for character development. His journey from seeking revenge to finding his own path in the Naruto series can be further explored in a fanfic.
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.