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.
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 common theme is power and ambition. Both Madara and Obito are characters with great power and strong ambitions in the Naruto series, and fanfics often explore how their relationship is influenced by these aspects.
The theme of redemption also appears. Given some of the actions of Obito and Madara in the Naruto series, fanfics sometimes explore if they can find redemption in their relationship with each other. They might try to make up for their past mistakes through their connection in the fanfic.
A third option is 'The Alliance of Obito and Madara'. In this one, the author focuses on their combined power and how they could have ruled the ninja world together. It's full of action scenes and also has some deep emotional moments between the two characters.
In such a fanfiction, the story could take a very dark turn. Naruto's ideals of friendship and peace might be severely tested. He could be forced to question his own beliefs as Obito and Madara have very different outlooks. Maybe Naruto would try to change their minds, but it would be extremely difficult as they are both very set in their ways of achieving a new world order through more extreme means.
Fanfiction.net is also a good place to look for madara x obito fanfic. There are many different stories written by fans from all over the world. However, the quality may vary, so you might need to read the summaries and reviews before choosing one.