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.
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 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, 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.
It depends on the specific fanfiction. Some might have Naruto develop strategies or skills to overcome the paperwork challenge. Others might not focus on this aspect at all.
Naruto would win. He has a lot of experience fighting powerful opponents and has developed many powerful jutsu over time. He also has the willpower and the ability to adapt in battle. Shukaku is strong, but Naruto's intelligence and his ability to think on his feet would give him the edge.
One common theme is self - improvement. Both Sakura and Naruto are constantly striving to get better in these fanfics. For example, Sakura might be trying to improve her combat skills to be on par with Naruto. Another theme is friendship. Despite their rivalry, their underlying friendship is often explored. It shows that they can compete and still care for each other.