One possible reason is that the person may find the fan - made interpretations of the Pokemon world too far - fetched. For example, some fanfictions might give Pokemon abilities that are completely against the established rules in the official games or anime. This can be off - putting to those who like the consistency of the official lore.
One consequence could be that he might avoid any events or communities related to Pokemon fanfiction. He won't be interested in interacting with fans who are into it, which could create a bit of a divide between him and some parts of the Pokemon fan community.
It depends on your definition of 'smart'. Some fanfics for 'The Hating Game' offer creative and well-thought-out plotlines and character developments. But it can take some searching to find the ones that meet your criteria.
He might become withdrawn. Instead of being the energetic and outgoing Naruto we know, he could isolate himself from his friends and the village. This would change the whole dynamic of the relationships in the fanfic.
She might give him harsher punishments than other students for the same offenses. For instance, if Harry is late to class, she could give him detention while letting others off with a warning.
One common reason could be jealousy. Maybe in the fanfic, Steve has something that Bucky wants, like a certain power or a relationship with someone. Another reason might be that Bucky has been manipulated by a villain in the story to turn against Steve.
In some fanfics, there could be a misunderstanding. Suppose Kushina did something that Naruto misinterpreted as harmful to him or his friends. This misinterpretation could lead to his hatred. For example, if Kushina was involved in a mission that Naruto thought put the village at risk, but in reality, she had no choice.