It could be that in the fanfic's storyline, the Rookie Nine have made some choices that go against Naruto's ideals. For example, if they side with a character or a group that Naruto sees as wrong. This could lead to his hatred. Also, perhaps there has been some miscommunication among them, and Naruto takes it the wrong way, which gradually builds up his negative feelings towards them.
Another reason could be that the Rookie Nine have different goals or values that conflict with Naruto's. For instance, if they are more focused on self - interest rather than the greater good that Naruto is always striving for. This divergence in values might lead to Naruto's dislike and eventually hatred for them. And also, personal conflicts within the group that Naruto gets caught in the middle of could be a factor.
Maybe Naruto feels overshadowed by the Rookie 9 in the fanfiction. In the original series, Naruto has his own journey and development. If the fanfiction misrepresents his relationship with the Rookie 9 in a negative way, like making them seem better than him all the time, he could hate it.
It can create a negative association. If the fanfiction is popular enough, some people might start to think that Naruto's relationship with the Rookie 9 in the actual series is also bad, which is not true.
If Choji has a better jutsu for his size - increase, it could make him a more integral part of the team. His friends would see him in a new light and they might have more group strategies that revolve around his new power. Kiba and Akamaru's new transformation jutsu would make them a more formidable duo, and the others would respect their fighting ability more. This would enhance the overall camaraderie among the rookie nine.
For Hinata, Naruto might create a jutsu that helps her enhance her Byakugan's range and clarity even further. It could also have a defensive aspect where she can project a shield made of chakra visible only to those with the Byakugan. For Shino, a jutsu that makes his bugs more resistant to enemy jutsus and also gives them the ability to track opponents over long distances. For Sasuke, a jutsu that combines his fire - based attacks with lightning in a more seamless way, creating a new and more powerful element.
In a fanfic where Naruto is older than the Rookie 9, he may have a different role in the village. Maybe he is already on the council or has a more influential position. He could use his influence to give the Rookie 9 better opportunities. For instance, getting them access to more difficult and rewarding missions that would help them grow faster as ninjas. His age difference would also mean that he has more wisdom and could offer better advice on things like handling relationships within the team and with other villages.
One interesting 'Naruto Rookie 9 fanfic' could be about their early training days in more detail. For example, how they overcame their individual weaknesses. Another might focus on the relationships between the characters outside of the main plot, like how Ino and Sakura's friendship evolved during their free time. And there could be fanfics that explore what if scenarios, such as if one of the Rookie 9 had a different chakra nature from the start.
In some fanfics, the idea of Naruto hating Hinata might be a plot device to create drama. Maybe the writer wants to explore a different kind of relationship dynamic than the canon one. It could also be that the writer has a unique interpretation of the characters' personalities and how they might clash in certain situations.
Maybe it's because Aphrodite's powers and the way she uses them are at odds with Naruto's own beliefs. Naruto believes in self - improvement through training and facing challenges head - on. If Aphrodite uses her love - related powers in a way that seems unfair or goes against Naruto's sense of justice in the fanfic, he would dislike her. Like if she uses her powers to manipulate people's emotions for her own gain, which is something Naruto would oppose.