One possible storyline is a cross - over where the ninjas in Naruto are exposed to the equivalent exchange principle of alchemy. They might start using it in their training, like instead of just relying on chakra, they think about what they are giving up to gain a new skill. For instance, a ninja might give up some of his speed to gain more strength. In the case of the Fullmetal Alchemist characters in the Naruto world, they could be involved in the battles between the villages. Alphonse could use his armor body to protect the villagers from attacks. And Scar from Fullmetal Alchemist could have an interesting interaction with the shinobi, as his unique form of alchemy might be seen as a very different type of jutsu.
One interesting plot twist could be the alchemy of the Fullmetal Alchemist world interacting with the Dust in RWBY. For example, maybe an alchemist discovers a way to transmute Dust into something completely new and unexpected, which throws the balance of power in Remnant (RWBY's world) into chaos. Another could be a character from RWBY somehow getting involved in the Philosopher's Stone plot of Fullmetal Alchemist, leading to a race between different factions in both worlds to either obtain or destroy it.
Well, sometimes there's a plot twist where the Fuhrer is actually being controlled by an ancient alchemical force. This force has its own agenda and is using the Fuhrer's position to further its own goals, like gathering all the Philosopher's Stones in existence. It turns the whole political situation in the Fullmetal Alchemist world upside down and makes for a really engaging read.
One interesting plot twist could be the discovery that the Philosopher's Stone in the Fullmetal Alchemist world has a connection to the chakra system in Naruto. Maybe it could be used to enhance or disrupt chakra flow in a way that no one expected. Another could be a character from Naruto, like Naruto himself, accidentally using alchemy due to some strange cross - world magic. This would completely change the dynamic as he tries to figure out this new power while still having his ninja abilities.
Another could be a time - travel scenario where Naruto goes back in time and meets Rikudou Sennin. They then team up to prevent a great evil from ever arising in the first place. This would allow for a lot of character development and exploration of the Naruto universe's history.
One interesting storyline could be Naruto using the Sharingan to enhance his combat skills in a new and unexpected way. For example, he might combine his Rasengan with Sharingan - powered genjutsu to create a more powerful and deceptive attack.
One interesting storyline could be the combination of Naruto's ninjutsu with Final Fantasy 7's materia system. Imagine Naruto using materia - enhanced jutsus. Another could be Cloud and Naruto teaming up to fight a common enemy like Sephiroth and Madara combined. It would be epic to see their different fighting styles blend.
One possible interesting storyline could be a female Naruto ending up in the Bleach universe and learning about the different spiritual powers there. She might try to adapt her ninja skills to the new environment filled with Hollows and Soul Reapers. Another could be a Bleach character getting transported to the Naruto world and being amazed by the chakra system. For example, Ichigo might be curious about how chakra is different from his reiatsu.
One idea could be that Naruto somehow ends up in the world of Fullmetal Alchemist and his chakra-based attacks are mistaken for some form of alchemical explosions. For example, his Rasengan could be seen as a condensed form of alchemical energy that explodes on impact.
One interesting concept could be the alchemy - ninjutsu fusion. Imagine Naruto characters using alchemical principles in their jutsu, like transmuting elements in a more alchemical way. Another concept might be the exchange of knowledge between the two worlds. For example, the alchemists teaching the ninja about equivalent exchange in combat strategies.
There probably are. Fanfiction writers often love to mash up different universes. In such a fanfic, Naruto could bring his chakra - based powers and blend them with the principles of alchemy from Fullmetal Alchemist. Maybe he'd use his Rasengan in a new way by incorporating alchemical transmutation circles. It would be a wild and creative concept.