Another option for the main characters could be Kaiba from Yugioh. His pride and determination would make for an interesting dynamic when faced with the neglect from the Naruto world. And from Naruto, Sasuke could be involved. He might initially see the Yugioh characters as a distraction from his own goals, but later on, things could change.
One possible plot could be that in a crossover world, the Yugioh characters are somehow transported to the Naruto universe. However, the Naruto characters neglect them, thinking they are just strange intruders. The Yugioh characters then have to find a way to get back home while dealing with the indifference of the Naruto world.
The jailer and an old, wise shinobi could be the main characters. The old shinobi used to be a great hero but now is retired. He sees the same potential in the jailer that he once had. He mentors the jailer, teaching him old techniques that were forgotten. Together, they face a new threat to the village that the other shinobi are ill - equipped to handle.
Sasuke could be one of the main characters. He might be initially suspicious of the neglected emperor, thinking he could be a threat to the balance of power. But as the story progresses, he could come to understand the emperor's situation. Another character could be Kakashi. He would likely be the voice of reason, trying to analyze the situation objectively and guide Naruto and the others in dealing with the emperor.
The obvious main character would be the neglected Anbu prodigy. He could be someone with a tragic past that led him to the Anbu in the first place. Another important character could be Naruto himself. Even though it's about the neglected prodigy, Naruto's presence is what causes the neglect, so he would play a significant role in the story.
Another option could be Naruto and Kaiba. Kaiba is a very proud and powerful character in Yugioh. He might initially view Naruto's situation of being neglected as a sign of weakness. But as the story progresses, he could see Naruto's determination and strength. Their interactions could be full of clashes at first, but then they could find common ground in their pursuit of power and recognition. Naruto would be trying to regain his status among his peers, and Kaiba would be constantly aiming to prove himself as the best duelist.
I'm not sure specifically as it's a fanfiction and can vary greatly. But it could potentially have Naruto characters like Naruto himself or Sasuke, combined with some Tokyo Ghoul characters like Kaneki. Maybe there are also some original characters created for this fanfiction.
Obviously, Naruto is one of the main characters. Since it's related to him being involved with a neglected god. The neglected god itself is also a main character, as the whole story revolves around its relationship with Naruto. There might also be other characters like Sasuke or Sakura who could be involved in different ways. For example, Sasuke might be suspicious of Naruto's newfound connection with this god and it could cause some tension between them.
It could be that some of the neglected characters from Naruto, like Rock Lee for instance, are made main characters in this fanfiction and are paired with a Gremory character. Maybe a Gremory character who also has been somewhat overlooked in their own series. This would give a new perspective and new storylines to explore.
Sasuke could be a main character as well. Given his own experiences of being an outcast and having a thirst for power at times, he could relate to Madara in some ways. They might form an unexpected alliance or have a rivalry based on their shared experiences of feeling neglected or misunderstood in the ninja world.
It could be a young and ambitious Kiri ninja who has grown up seeing the neglect of his village. He might be determined to change the situation and prove that Kiri is not to be underestimated. Maybe he has a special jutsu or ability that he believes can put Kiri back on the map.