The most common themes include the exploration of different cultures. Naruto has its own ninja culture, while Fate Stay Night has the mage and servant culture. Fanfics usually show how these two cultures clash and blend. Destiny is also a big theme. Given the importance of destiny in both series, in the fanfics, characters often question or try to change their fates. Moreover, self - discovery is a theme. Characters from both sides discover new aspects of themselves when exposed to the other world's situations and characters. This can lead to interesting character development throughout the fanfic.
One common theme is the clash of power systems. Since Naruto has chakra - based powers and Fate Stay Night has magic, seeing how these two different types of powers interact or conflict is often explored. For example, in many fanfics, Naruto might try to use his chakra to counter a magical attack from a Fate character.
One interesting Fate Stay Night Naruto fanfic is 'Naruto in the World of Fate'. In this fic, Naruto is somehow transported to the Fate Stay Night universe. It's really cool to see how his ninja skills interact with the magic and combat system in the Fate world. Another one could be 'Fate Servants in Konoha' which imagines what would happen if Fate's Servants showed up in Naruto's village.
I really like the fanfic 'Rin's Redemption'. It focuses on Rin's character development in a way that the original might not have fully explored. The plot is filled with twists and turns that keep you hooked from start to finish.
One idea could be to have Naruto characters participate in the Holy Grail War. For example, Naruto himself could be a Servant, perhaps with his chakra being a unique form of mana. His skills like the Rasengan could be reimagined as powerful Noble Phantasms. Another idea is to put the Fate Stay Night characters in the Naruto world. They might have to deal with things like ninja clans and the politics of the hidden villages while also trying to find a way back to their own world.
One popular 'naruto and fate stay night fanfic' is 'Naruto in the World of Fate'. It combines the unique ninja elements from Naruto with the magic and servant system of Fate Stay Night. Another one could be 'Fate's Ninja', which often has interesting crossovers in terms of character interactions, like Naruto meeting Saber and having to fight together against a new threat that combines the evils of both worlds.
One way could be to create a crossover universe where Mordred from Fate Stay Night somehow ends up in the Naruto world. Maybe she could be a new kind of ninja with her own unique abilities based on her Fate Stay Night powers. For example, her sword skills could be translated into a new form of kenjutsu in the Naruto world.
In a crossover, the power systems would likely have to be balanced. The jutsu in Naruto are very different from the magic in Fate Stay Night. However, if a Fate character were to enter the Naruto world, they might find that their magic is affected by the chakra - rich environment. For instance, a mage's fire spell might be enhanced by the natural energy in the Naruto world. On the other hand, a ninja using chakra might find that they can learn some basic magic concepts from the Fate characters and use it to supplement their jutsu.
A plot could be that Mordred is summoned by a powerful ninja as a last - ditch effort to fight against an ancient evil that has emerged in the Naruto world. This evil has powers similar to some of the powerful Servants in Fate Stay Night, so Mordred's expertise is needed.
There's 'Fate's Ninja'. It focuses on how the ninja skills from Naruto's world can be combined with the magic and concepts in Fate Stay Night. The story has a lot of character development for both Naruto characters in the Fate universe and vice versa, showing how they learn from each other's worlds.