There could be a shift from enmity to a begrudging respect. Madara has always been a powerful and feared foe, but with Naruto being stronger, Madara may have to accept Naruto's superiority. Naruto, on the other hand, would likely try to understand Madara's motives better and might try to reform him rather than just defeat him.
Well, if Naruto were Madara's grandson in fanfiction, it could completely change the power dynamics. Naruto might have access to different jutsu from the start. For example, he could potentially inherit some of Madara's unique Sharingan abilities or his knowledge of ancient Uchiha techniques. This would make him even more formidable early on and might change how his relationships with characters like Sasuke develop. Instead of a rivalry based on the Uchiha massacre, it could be more about Naruto trying to guide Sasuke using his Uchiha heritage.
Their relationship would likely shift from being enemies to something more complex. Naruto's help might make Madara view him as an equal or even a friend. Madara, who has been alone in his ideology for so long, might start to respect Naruto's different perspective on peace.
The plot could change drastically. For one, the power balance in the ninja world would be severely disrupted. Enemies that were once a threat would be easily dealt with. The fusion could also change the political situation. With its combined charisma (from Naruto) and intimidating presence (from Madara), it could unite or divide the villages depending on its goals.
Naruto would probably get Madara's Sharingan abilities. This could give him enhanced perception and the ability to copy jutsu more easily, like a supercharged version of his own ability. He might also gain access to Madara's Susanoo, which would be a huge boost to his combat capabilities.
Well, in such a fanfiction, Madara's training might enhance Naruto's physical strength. He could teach Naruto some advanced Uchiha techniques which Naruto can combine with his own Uzumaki powers. For example, Naruto might learn better chakra control from Madara, enabling him to use his Rasengan more effectively and with less chakra waste.
His relationship with Sasuke would be really interesting. Since Sasuke has his own complex connection to the Uchiha clan and Madara, Naruto becoming a Madara fan could either bring them closer together in understanding the Uchiha's past or drive them further apart if Sasuke doesn't agree with Naruto's new - found admiration. Maybe Naruto would start to push Sasuke towards a more 'Madara - like' view of power and revenge.
If Naruto kills Madara in fanfiction, it could completely shift the power dynamics in the Naruto universe. For one, it might lead to a more peaceful era much sooner as Madara was a major source of conflict. The Akatsuki's plans would likely fall apart without his influence, and the shinobi villages might start to focus more on internal rebuilding and cooperation rather than external threats.
The story would change drastically. Naruto's identity as a descendant of Madara would immediately put him at odds with some in the village who still fear the Uchiha. His journey to become Hokage would be even more challenging as he has to prove that he's not going to follow in Madara's footsteps. Also, his training might take a different route. He could be taught some ancient Uchiha techniques by an unexpected mentor, perhaps an old Uchiha who has been in hiding.
For Naruto, being trained by Madara could mean he learns how to counter Uchiha - specific techniques more effectively. His physical strength might also increase due to the intense training. Sasuke would be able to better harness his hatred and turn it into a more focused power source. Madara's teachings could expose them to ancient jutsu and knowledge that would give them an edge over their enemies. Their teamwork might also be affected, as they would both be influenced by Madara's way of thinking.