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 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 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 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.
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 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.
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.
Maybe the main antagonist is the entire Iwa council. They might be the ones who order Naruto's abandonment because they fear his potential influence on Iwa. They would do everything in their power to keep him from uncovering their plans or causing unrest among the villagers.
Maybe in the 'naruto neglected iwa fanfiction', there's a story where Iwa has a secret technique that could have been useful in the great ninja wars, but because they are neglected, they are not invited to share this knowledge. As a result, a young Iwa ninja goes on a journey to find a way to make the other villages recognize their worth and the importance of their techniques.
The main antagonists could be some of the conservative Iwa ninjas who oppose Naruto joining their village. They might see him as a threat to their traditional ways and values. Also, there could be some rogue ninjas from other villages who target Naruto because they see him as an easy target now that he's in a new and unfamiliar environment.