Well, it depends on the specific fanfiction. There are various interpretations out there. Some fanfictions focus on Naruto's growth after the original series and give him abilities like super - charged chakra control or the ability to nullify Madara's strongest jutsu. However, in the original canon, Madara is an extremely powerful opponent. But in fanfiction, the rules can be bent to make Naruto stronger.
Well, it depends on the specific fanfic. Some fanfictions might give Naruto an edge over Madara by, say, having him master some super - secret jutsu that completely nullifies Madara's powers. Or they could boost Naruto's physical and chakra capabilities to an extent where he can easily defeat Madara. However, in the original Naruto lore, Madara is an extremely powerful foe, but fanfic authors have the freedom to change the power balance as they see fit.
In fanfiction, Naruto can be stronger than Madara for multiple reasons. Some authors might want to subvert the expectations set by the original story. They could give Naruto unique abilities like the ability to manipulate time, which would clearly put him above Madara in terms of power. Additionally, it could be a way to bring in crossovers. For instance, if Naruto gains powers from another fictional universe, he could easily be made stronger than Madara. Moreover, the author may simply want to explore a scenario where Naruto is the most powerful character, and making him stronger than Madara is a step towards that.
In a lot of fanfics, Naruto is stronger than Sasuke. Naruto has always had an incredible willpower and in fanfics, this can be translated into him achieving greater power levels. His ability to make friends and allies can also lead to him getting more support and resources in the story. For example, he might get some special training from an ancient sage that Sasuke doesn't have access to. Also, his positive attitude can attract more powerful beings to help him out, which gives him an edge over Sasuke in terms of strength.
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.
One reason is that Naruto has the Nine - Tails' chakra. In fanfic, this power can be further enhanced or manipulated in ways that make him far more powerful than Sasuke. Another reason could be his more outgoing personality. He might be able to form alliances more easily, leading to him having more resources and power - ups at his disposal.
Naruto is stronger in fanfiction because of his ability to connect with others. He has made friends all over the ninja world. This network of friends often provides him with support in battles, whether it's intel or actual combat help. Also, his training under Jiraiya was very comprehensive. Jiraiya taught him not only combat skills but also how to be a better person. This made Naruto grow both physically and mentally. And compared to Sasuke, Naruto seems to be more adaptable to different fighting styles in fanfiction, which gives him an edge in combat.
The relationship might become more equal. Since Sakura is stronger, Sasuke can't look down on her as he might have in the original story. They could become more like true partners, respecting each other's abilities.
Another plotline might be Naruto's strength leading to a different kind of peace in the ninja world. Since he's stronger, he can enforce his ideals more effectively. He could start a new era of cooperation among the ninja villages by using his power to make the other villages see the benefits of unity, and Sasuke might be reluctantly following his lead.