In this type of fanfic, it could be that Naruto's sister is ill or has some special condition that requires a lot of care from their parents. So, Naruto is pushed to the side. However, Naruto being Naruto, he still tries to find his own way in the ninja world. He might find a mentor outside of his family who sees his potential and helps him grow. Eventually, he could come to terms with his family's situation, or they could realize that they've been neglecting him and try to make amends.
Well, one possible interesting plot could be the exploration of a darker Naruto who has been pushed to the edge by neglect. Maybe he forms unexpected alliances with characters usually considered antagonists in the original story, like Orochimaru, but for different motives than in the canon. He might be seeking power not just for himself, but to expose the flaws in the ninja system that led to his neglect.
Another storyline could involve Naruto's sister being trained more rigorously by the village elders because they see more potential in her. Naruto, feeling neglected, then goes on a self - discovery journey to find his own strength outside the village's traditional training methods. As he grows stronger, his sister realizes the mistake of the elders and tries to make it up to Naruto.
A possible plot is that the neglected twin sister is actually a key to an ancient prophecy that the village doesn't know about. As she grows up, she starts to have strange dreams related to the prophecy. She then embarks on a journey to figure out what it all means. Along the way, she befriends some unlikely allies, like a group of rogue ninjas who have their own reasons for helping her. In the end, she reveals the truth about the prophecy and her importance to the village, which makes Naruto and the others regret their neglect.
One possible storyline could be that Naruto, feeling constantly neglected, decides to leave Konoha in search of a place where he can be truly accepted. He might stumble upon a hidden village that has its own unique ninja culture and there he begins to train in new and different ways, far from the scorn he faced in Konoha.
Another aspect could be the relationship between Naruto and his sister. If she is the favored one, she might initially be oblivious to Naruto's pain. But as the story progresses, she could realize how wrong it is and try to make it up to him. This could lead to a complex family dynamic exploration in the fanfiction.
A plotline might involve Naruto starting to act out in negative ways to get his parents' attention. He could start getting into trouble at school or in the village. Maybe he would start to explore his own powers in secret, away from his family, and discover some unique abilities that he then uses to show his parents what they've been missing. Also, there could be a plotline where Naruto tries to build a relationship with his sister in secret, hoping that through her, he can get closer to his parents.
One possible plot could be that Naruto's sister is seen as more talented or important in the ninja world. For example, she might be a prodigy in a certain jutsu that Naruto struggles with. So, the village focuses all its attention on her, leaving Naruto feeling ignored. Another could be that she has some special power or connection that makes her the center of attention, and Naruto is constantly overshadowed by her in every aspect, from training opportunities to social recognition.
It could be that his sister has some special abilities or talents that the family or the village values more. For example, if she has a very rare and powerful bloodline limit, everyone's attention would be drawn to her. In a ninja world, power and potential are highly regarded, so Naruto might be overlooked because his sister seems to have more of that 'special something' at first glance.
One possibility could be an original character created specifically for the fanfiction. This gives the writer the freedom to shape her personality and backstory completely. Another could be a minor character from the Naruto series that doesn't get much attention, like Tenten's sister if she had one. It could also be a reimagined version of Hinata as Naruto's sister. Since Hinata has her own story in the original series, reimagining her as Naruto's sister with a neglected past could lead to some interesting fanfiction ideas.
One key theme could be family dynamics. Since Naruto is neglected, it might explore how his sister could potentially change his situation or their relationship. Another theme could be self - discovery. Naruto may find new aspects of himself with his sister's influence. Also, it might touch on the theme of redemption, perhaps for those who neglected Naruto in the first place.