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.
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.
Another plot could be that the neglected harem characters start to suspect that Naruto is actually interested in someone outside the harem. So they begin to investigate, spying on his every move and getting into all sorts of comical and also somewhat tense situations as they try to figure out who this mystery person might be, all while still hoping for Naruto's attention.
Well, one possible plot could be that the neglected god decides to test Naruto in secret ways. For example, it might create some strange challenges in the Hidden Leaf Village that only Naruto can sense. Another plot could involve the god being neglected because of some old grudges in the ninja world, and Naruto unknowingly becomes the key to resolving this and restoring the god's proper place. There could also be a plot where the neglected god has a special power that Naruto needs to unlock his true potential.
A third plot might be that she gets kidnapped by an outside force that wants to use her as leverage against Cross Academy. This would then lead to Zero and the other students embarking on a rescue mission. Along the way, they discover more about her past and the secrets that her existence holds, which could change the dynamics of the entire academy.
Her character might develop through self - discovery. Since she's neglected, she has to rely on herself. So she starts exploring her own strengths and weaknesses. For example, she might find out that she's really good at stealth because she's always had to hide her feelings. As she faces various challenges, like dealing with bullies in the village or trying to prove herself to her family, she becomes more confident and assertive.
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.
At first, the relationship might be strained. Naruto could be jealous of his sister's favored status. However, as the story progresses, his sister might start to see the injustice Naruto faces and try to bridge the gap. They could gradually develop a more understanding and loving relationship.
One interesting plot could be the twin sister having a special magical ability that Harry doesn't. For example, she might be able to communicate with magical creatures in a way no one else can. This could lead to her helping Harry in his adventures in a unique way, like getting help from a phoenix or a centaur when they are in a tough situation.
One interesting plot could be that the wolf summons, feeling neglected, form their own clan within the forest. They start to develop unique abilities separate from Naruto's influence. For example, they might learn to communicate with other forest animals in a more complex way to protect their territory.
One interesting plot could be where the neglected and dark Naruto is thrust into a crossover with another anime world, like Bleach. He could use his new - found darker powers to fight Hollows, and his experiences of being neglected could add depth to his character as he tries to find his place in this new world. Maybe he forms an unlikely alliance with a Soul Reaper who also has a troubled past.