One possible storyline could be a character who has been rivals with Naruto for a long time. They hate him because he always seems to outshine them, but deep down they love him because they see his kind heart. For example, Sasuke might have such complex feelings. He hates Naruto for being so persistent in bringing him back to Konoha, yet he also loves Naruto as his true friend who never gives up on him.
One reason could be that some fans are very purist about the original Naruto story. They might feel that fanfiction often distorts the characters or the plot in ways that go against the essence of what Naruto is all about. For example, changing a character's personality completely to fit a romantic or dark and edgy narrative that doesn't align with the source material.
The different power scales. Naruto has his own progression of power through training and ninja ranks. Superman's power is on a completely different level like being able to move planets. In fanfiction, it might be hard to balance their powers in a way that makes sense to Naruto fans, so Naruto might seem to 'hate' it.
Perhaps in fanfiction, Boruto is associated with a group or ideology that Naruto opposes. This could cause Naruto to view Boruto unfavorably. Also, if there are false rumors or misinformation spread in the fanfiction world about Boruto, Naruto might believe them and start to hate Boruto until the truth is revealed. And sometimes, it's just a way for the writer to make an interesting and unexpected plot twist.
In a Naruto and Derieri fanfiction, a possible storyline could be that Derieri is mistaken for an enemy in the Naruto universe. Naruto, being the one to see her potential for good, tries to convince others that she is not a threat. As they try to clear her name, they uncover a conspiracy that threatens both their worlds. This would involve a lot of mystery - solving and action as they race against time to stop the conspiracy.
One possible storyline could be that Naruto is chosen as a temporary Kazekage due to a threat that requires his unique skills. He then has to deal with internal conflicts within the Sand village while also facing external enemies. Another could be that there is some kind of prophecy that only Naruto can fulfill as Kazekage to save both Konoha and Suna.
A storyline could involve Naruto using his newfound Nara abilities to solve a mystery in the village. Maybe there's a strange phenomenon that's related to shadow - based jutsu, and Naruto, with his understanding of both Uzumaki and Nara powers, is the only one who can figure it out. He'd have to team up with other characters, and in the process, there would be a lot of character development and interesting interactions.
Another storyline might be that Millet is a secret organization in the Naruto world. Naruto discovers that this organization has been pulling the strings behind some of the conflicts. He has to infiltrate it and expose their true motives. This would be a great opportunity for Naruto to use his stealth and combat skills, as well as his ability to make friends and allies within the organization to bring it down from the inside.
One possible storyline could be Naruto as an elf trying to fit into the ninja world while still having his elf heritage. He might face discrimination from some who don't understand his different nature.
One possible reason could be a misunderstanding. Maybe some false information was spread about his mother, making Naruto believe she had abandoned him. Another reason could be related to the secrecy around his mother. If he grew up feeling alone and not knowing about her, he might develop resentment.
One reason might be that he doesn't like how fanfiction can change the relationships between characters. For example, in the original, his relationship with Naruto is based on training and mentorship, but fanfiction could make it something completely different.