There might be. In the Naruto series, both Naruto and Nagato have complex backstories. If they were brothers in a fanfic, it would be really interesting. Maybe Naruto could have influenced Nagato to take a different path earlier. For example, Naruto's positive attitude towards life and his belief in peace could have rubbed off on Nagato, preventing him from going down the more violent routes he took in the original story.
One possible plot could be that they grow up together in a small village. Naruto's positive influence makes Nagato less likely to be influenced by Madara's ideas later. They both train under Jiraiya, and together they try to bring peace to the ninja world in a different way than in the original story.
In these fanfics, Nagato may help Naruto on an ideological level. Nagato once believed in a very different way of achieving peace. By sharing his journey and how he came to realize the flaws in his thinking, he can guide Naruto in his pursuit of true peace. Nagato could also use his influence over the Akatsuki remnants to prevent them from causing more chaos, which in turn helps Naruto in his mission to protect the ninja world.
In a fanfic where Naruto takes Nagato's eyes, he might gain new and powerful abilities. For example, he could potentially access the Rinnegan's powers more directly. This could make him even stronger in combat, perhaps allowing him to use abilities like the Six Paths Techniques with greater ease. It could also change his relationships with other characters. Some might be in awe of his new power, while others could be afraid or jealous.
Well, it could be that Naruto and Nagato initially engage in a fight as they have different ideologies. But then, as they talk more, they might find common ground. Maybe Naruto tells Nagato about his dreams for peace in the ninja world, which makes Nagato re - evaluate his actions. And Nagato could also share his past with Naruto, explaining why he came to his current beliefs.
He could be more light - hearted. Instead of being burdened by his past immediately, he might start off with a more positive outlook. For instance, he could be curious about the new world around him and approach things with a sense of wonder.
One possible plot development is that Nagato and Naruto form an alliance to take on a new, greater threat. This threat could be an ancient evil that requires both Nagato's power and Naruto's spirit. Another development could be Nagato using his abilities to help Naruto unlock new powers or forms. For example, he might help Naruto better understand the Sage of Six Paths' power within him.
One main theme is redemption. Nagato has done a lot of bad things in the Naruto series, and in fanfics, often Naruto is the catalyst for his redemption. For example, Naruto's talk - no - jutsu can make Nagato see the error of his ways.
Well, 'A New Beginning for Nagato' is also a great 'naruto x nagato fanfic'. It starts with Nagato being given a second chance at life by some mysterious force. Naruto, sensing this, approaches Nagato and they start to work together to rebuild the Rain Village. The fic focuses on their growing friendship and how they use their combined powers for the good of the village.