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 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.
In some fanfics, characters from other universes might initially be in awe of the Fuhrer due to his power and status. They could approach him with caution, trying to figure out if he's an ally or a threat. For example, a character from a magical universe might be intrigued by the alchemical powers in the Fullmetal Alchemist world and see the Fuhrer as a key to understanding it all.
Well, a great plot twist might be that the characters from Fairy Tail end up in the world of Fullmetal Alchemist and are mistaken for some sort of alchemical creations. They then have to prove that they are not and in the process, they discover that their magic has some strange effects on the alchemy in that world. For example, Gray's ice magic could freeze alchemical reactions in unexpected ways. Another plot twist could be that the Gate in Fullmetal Alchemist has a link to the Fairy Tail's Celestial Spirit World. So when someone tries to open the Gate, they accidentally open a portal to the Celestial Spirit World instead, and all kinds of chaos ensues as spirits and alchemists meet for the first time.
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.
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 if the alchemical principles in Fullmetal Alchemist were somehow applied to the use of the Rinnegan in Naruto. For example, the Rinnegan's powers being transmuted or enhanced in a way not seen in the original Naruto series.
Well, in some fanfictions, a plot twist is that the harem members start to lose their memories of Naruto. This throws the whole group into chaos as Naruto tries desperately to make them remember. It could also be that a new character enters the harem from an unexpected source, like a crossover within the Naruto universe that has an impact on the Fullmetal Alchemist elements. For example, a powerful shinobi with alchemical knowledge shows up. And sometimes, a plot twist is that the alchemy in the world starts to behave in a strange way that only Naruto can somehow fix, which changes the power balance in the harem and the relationships.
A common theme is the clash of different power systems. Alchemy and magic are very different, and seeing how the characters from each world react to the other's power source is interesting. For instance, wizards might be amazed at the physical transformations possible through alchemy.
One of the most interesting plot twists could be the sharing of powers. For example, Naruto's ability to use chakra might combine with the unique demonic powers in Highschool DxD in unexpected ways. Maybe a character from Naruto's world gains a devil fruit - like ability from the Highschool DxD universe. Another could be a character from Highschool DxD learning how to use ninjutsu, which would completely change the power dynamics in their own world.
One idea could be to have Bradley cross over into a modern - day world. He'd be out of his element, dealing with things like technology and modern social norms. It could be funny to see his reaction to things like cell phones or cars.