I think it's a toss-up. Deku has potential and is constantly evolving, but Naruto's strength and strategic thinking give him an edge. It could come down to the specific circumstances of the fight.
Naruto's outgoing and boisterous personality would make Deku more confident. He would probably be more upfront and less shy. Naruto's strong sense of justice would also intensify Deku's already existing desire to help others.
I think Hinata could be an ally. She has always been in love with Naruto and would not stand by while he is in danger from Dark Naruto. Additionally, Shikamaru is smart and strategic. He might see the threat of Dark Naruto to the village and decide to assist Naruto, using his intelligence to come up with battle plans.
In a fanfiction where Naruto is reborn as Deku, there would be a lot of potential for unique storylines. Naruto's experience with facing powerful enemies in the Naruto world could give Deku an edge. He might be more aggressive in battles compared to the original Deku. Also, Naruto's ability to make friends and form bonds could strengthen Deku's relationships with his classmates even further. And his understanding of power and how to grow stronger could lead to a faster development of Deku's abilities.
In fanfiction, the Rinnegan is often depicted as more powerful than the Sharingan in many ways. The Rinnegan has abilities like the Six Paths techniques which can be extremely overpowered. For example, it can allow the user to control gravity, summon large creatures, and even revive the dead. While the Sharingan has its own set of cool abilities like predicting movements and casting genjutsu, it seems limited in comparison when it comes to the grand scale of power shown by the Rinnegan in most fanfictions.
In a fanfiction, the aliens could capture Naruto and try to study his unique abilities. The monsters then decide to rescue him because they realize his powers could be the key to defeating the aliens once and for all. The story could involve a lot of action as the monsters infiltrate the alien base to save Naruto.
Well, perhaps the plot could revolve around a tournament. In this 'naruto luffy deku crossover fanfiction', they all enter a huge, multiverse - wide tournament. Naruto shows off his cool jutsu, Luffy surprises everyone with his stretching attacks, and Deku displays his newfound strength. Along the way, they have to team up against some really tough opponents who don't play fair, and they grow closer as friends.
Well, sometimes in 'naruto vs dark naruto fanfiction', a cool plotline is when Dark Naruto has some new powers that Naruto has to figure out how to counter. For example, Dark Naruto might be able to control shadows in a way that Naruto has never seen before. Or perhaps Dark Naruto has allied himself with a powerful dark force from outside the ninja world. Naruto then has to not only battle his dark self but also this new threat.
The main differences are in their expressions and some minor details of personality. In the manga, Deku might seem a bit more intense, while in the anime, he's sometimes presented a bit softer.
It's really hard to say. Naruto has the power of the Nine - Tails and all his ninja training. Luffy has his Devil Fruit powers and his unwavering will. Deku has One For All which gives him incredible strength. But if I had to choose, I might say Naruto. His ability to create thousands of clones and use powerful jutsu like Rasengan could give him an edge in many battles.