One possible plot twist could be that her family has a secret reason for neglecting her. Maybe they're trying to protect her from some greater danger. Another could be that she discovers she has a hidden power that makes her family regret their neglect.
Perhaps the Akatsuki's neglect is a part of a much larger plan by Naruto himself. He might be trying to lull the Akatsuki into a false sense of security while he's actually gathering information or power in the background. Then, when the Akatsuki least expects it, Naruto reveals his true intentions and uses the situation to his advantage, which would be a huge plot twist for the readers who thought Naruto was just being mean or indifferent.
A plot twist might be that Naruto, after being abandoned by his family, finds a new 'family' in unexpected places. For example, he could bond closely with a group of outcasts in the village who understand his pain. Or perhaps, the family's abandonment was part of a larger conspiracy within the ninja world, and Naruto's journey to uncover the truth behind it becomes a major part of the story.
One possible plot development could be Naruto exploring his new bloodthirsty nature and how it affects his relationships with his friends. Maybe at first they are scared, but then they try to understand him. Another could be Naruto seeking revenge on his family for neglecting him, which might lead to some intense confrontations. And finally, he could find a new family among his comrades who accept him for who he is.
A plot twist could be that Naruto discovers that his family's neglect was actually part of a bigger scheme. In the harem fanfiction world, perhaps someone was manipulating his family to keep Naruto down so that they could have an advantage in the competition for Naruto's affection in the harem. This revelation would completely change Naruto's view of his family and the situation he's in.
Well, a typical plot twist is that Naruto leaves the village due to the neglect. He then returns as a much stronger and more mysterious figure. This forces his family to re - evaluate their actions. Another common plot twist is that the sister is actually in danger, and Naruto is the only one who can save her, despite the family's past treatment. It flips the situation and shows that Naruto is still the bigger person. And sometimes, a plot twist could be that Naruto has a secret heritage that was the real reason for the family's strange behavior towards him.
One possible plot twist could be that the gun magic is actually a curse in disguise. Maybe it seems powerful at first, but it slowly starts to corrupt Fem Naruto, and she has to fight against its dark influence.
In a fem Naruto neglected fanfiction, a possible plot could be that she is constantly overlooked for important missions. As a result, she takes on her own self - assigned missions to prove her worth. Along the way, she discovers a hidden power within herself that is related to her female identity and the Nine - Tails, which she uses to save the village in a time of great crisis.
A plot twist could be that fem Tsukune is actually a long - lost relative of a powerful Naruto character. Maybe she has some special bloodline that links her to someone in the Naruto universe, and this discovery changes the whole dynamic of the story.
One plot twist could be that Naruto discovers his parents had a very good reason for their neglect, like they were protecting him from a greater danger. Another could be that the village elders knew about the neglect but did nothing, and Naruto has to confront them. Or perhaps Naruto finds out he has a secret power that was the cause of his parents' seeming neglect, as they were afraid of what he could do.
One possible plotline could be Naruto finding a new family in the crossover world. For example, if it's a crossover with the Harry Potter universe, he might be taken in by the Weasley family who see his potential and give him the love and support he never had in his own family. Another plotline could be Naruto using his skills to prove his worth to his neglectful family after being influenced by the new world he's in. He could return to his own world with newfound confidence and make them realize what they missed out on.