It might be Naruto himself. Imagine Naruto stumbling upon the dragon that everyone else has ignored. He, with his kind heart and sense of justice, would likely try to understand and help the dragon, which could lead to a whole new adventure for him.
Another possibility is that the main character could be an outcast ninja. Since the dragon is also neglected, they might find common ground. This outcast ninja could see the value in the dragon when no one else does and together they could strive to change their fates in the Naruto world.
It could be a new character created specifically for the fanfiction. Maybe a young ninja who discovers the neglected dragon and forms a bond with it.
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.
Maybe an outcast ninja. This person has always been on the fringes of the ninja society. Discovering the neglected sword gives them a chance to prove themselves. They could be someone with a lot of untapped potential who uses the sword to rise above the neglect they've faced.
It could be Samehada itself. Since the story is about it being neglected, it makes sense for it to be the main focus. It could have its own 'voice' and thoughts as it tries to deal with the situation.
It could be an orphan who has a natural talent for music but has been brought up in a ninja - dominated environment where music is seen as a useless skill. So, they are constantly neglected.
It could be an unknown Uchiha who was overlooked in the main story. Maybe they were born with the Rinnegan but due to some political unrest in their village, they were forced to hide their power and were thus neglected. In the fanfiction, they could come out of hiding and shock everyone with their Rinnegan - based abilities.
It could be a young Saiyan who was sent to the Naruto universe as part of some sort of experiment by the Saiyan race. They are neglected because they seem so different from the ninjas. They would be the main character as they struggle to find their place and purpose in this new world.
A young and talented Iwa ninja who feels left out could be the main character. He or she might be frustrated with how their village is always in the shadow compared to Konoha and wants to change that perception.
It could be Orochimaru. In this fanfiction, Orochimaru might hear rumors about the Dragon Balls and their power to grant wishes. Since he is always seeking power and immortality, he decides to hunt for the Dragon Balls. However, because Naruto is so focused on his own battles against Orochimaru in the ninja world, he fails to realize that Orochimaru's new goal involves the Dragon Balls and the entire Dragon Ball Z universe could be at risk.
Sasuke could also be a great main character in this fanfiction. Given his drive for power, he might be the one to seek out the dragon armor and use it to further his own goals. He could have an interesting journey of learning to control the power of the armor while also dealing with his inner demons.
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.