Maybe it's an old enemy of Uzuki's who has resurfaced. They see Naruto as a threat because of his potential and Uzuki's training is making him even stronger. This antagonist could have some dark powers or be a master of a forbidden jutsu. They might try to kidnap Uzuki to force Naruto to come to them or try to corrupt Naruto during the training.
Another possibility is that the main antagonist is a group within Konoha who don't want Naruto to become too powerful. They fear that Uzuki's training will make Naruto uncontrollable or a threat to their own power within the village. So they try to undermine the training by spreading rumors or causing internal conflicts.
It could be a rogue ninja from another village who has a grudge against Uzuki and wants to stop her from training Naruto. This ninja might be jealous of Uzuki's skills or have some past conflict with her. They could try to disrupt the training sessions by attacking Naruto or setting traps.
The fanfic could also involve Uzuki training Naruto to control his chakra better. Naruto has always had an abundance of chakra but has struggled with control at times. Uzuki, with her experience, could teach him some advanced chakra control methods. This might include meditative techniques or special exercises. It could also introduce a new villain or threat that Naruto needs to face, and the training is his way to prepare for it.
There could be a group of bandits who have been causing trouble around the areas where Naruto is training Team 8. They don't like the idea of a strong team emerging in their territory. So, they start attacking the team during their training sessions. These bandits might have some crude but effective combat techniques and they also use the terrain to their advantage, which makes them a formidable antagonist for Team 8 during their training with Naruto.
It could be Frieza. Frieza might sense Gohan getting stronger under Beerus' training and see him as a threat. He decides to stop Gohan's progress by any means necessary.
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.