One possible scenario in such a fanfiction could be that Naruto's parents are preoccupied with their shinobi duties. They might be constantly on missions for the Hidden Leaf Village, leaving Naruto at home with caretakers who don't really pay him much attention. This could lead to Naruto feeling lonely and isolated, just as he did in the original story when he thought he had no family.
A possible plot could be that Naruto discovers that his parents' neglect is due to a secret they are keeping from him. They might be protecting him from a greater threat by staying away from him, but Naruto misinterprets it as neglect. As he digs deeper into the mystery, he uncovers the truth and has to decide whether to forgive his parents or not. This would add a lot of drama and emotional turmoil to the story.
In fanfiction, Naruto having the Rinnegan and being neglected by parents can lead to some really interesting character development. It could make him more self - reliant and distrustful at first. He might have to learn to harness the power of the Rinnegan on his own, without any parental guidance. This could result in him making some mistakes along the way but also growing stronger in unique ways.
One possible reason could be that they are too involved in their own shinobi duties. The world of ninjas is full of dangerous missions, and they might be constantly away on important tasks, leaving Naruto feeling neglected.
The story would be very different. Naruto's parents being alive would mean he has a support system from the start. His father could pass on his jutsu and wisdom more directly. Naruto might not have the same drive to become Hokage in the same way, as he wouldn't be seeking that family - like recognition from the village. His mother's presence would also add an element of warmth and stability to his life. And perhaps he would be more of a prodigy with both his parents' guidance, changing the power dynamics in the ninja world.
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.
A possible plot is that Naruto is constantly bullied because of his neglected state and his unknown bloodline. As he grows, he starts to show signs of his bloodline powers, which attracts the attention of both friends and foes. His journey then becomes about controlling his powers and dealing with the past neglect of his parents while also facing the new challenges that come with his revealed bloodline.
Naruto might try to seek attention elsewhere. He could focus on his training more intently. By pouring his energy into becoming stronger, he distracts himself from the pain of parental neglect. Also, his friends could play a crucial role. Their friendship might give him the sense of family and belonging that he lacks at home.
The exploration of Naruto's powers is crucial. Since he's godlike, his powers are likely to be extraordinary. His parents, being experienced ninjas, can help him understand and manage these powers. Also, the fanfiction might focus on how the ninja world reacts to a godlike Naruto with his parents alive. Some might fear him, while others might see him as a savior. This creates a complex web of relationships and storylines.
It has a huge impact. Naruto being neglected by his parents in crossover fanfiction can change the entire plot direction. Instead of having the usual drive to gain recognition from the village, he might be more focused on finding out about his parents and why they neglected him. This could lead him into different adventures and interactions. Maybe he'd be more likely to leave the village earlier in search of answers.