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.
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.
Edward Elric would be a very interesting choice. His brash and determined personality would clash and also blend well with the Fairy Tail mages. He could learn about the different types of magic in Fairy Tail and might even try to find a way to combine his alchemy with magic. His search for the Philosopher's Stone could also take an interesting turn in the Fairy Tail universe.
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.
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, consider Wendy's healing magic. In a crossover, she could use her magic to heal the wounds caused by alchemical experiments gone wrong or battles in the Fullmetal Alchemist world. In return, the alchemists could teach her about the properties of different herbs and substances that could enhance her healing magic. Gajeel's iron dragon slayer magic could interact with the metal - based alchemy. He could use his magic to shape and manipulate metal in ways that the alchemists find fascinating. And then there's Mirajane's transformation magic. She could transform into forms that are better suited to deal with the alchemical threats in the Fullmetal Alchemist world, while the alchemists could help her understand the physical and chemical changes that occur during her transformations.
One of the most popular crossovers might be those that focus on the magic systems. For example, combining the alchemy from Fullmetal Alchemist with the magic in Fairy Tail. Fans love to see how characters from both worlds would interact with these different power sources. Another popular type could be character - centered crossovers. Imagine Edward Elric from Fullmetal Alchemist teaming up with Natsu from Fairy Tail. Their different personalities and goals would create an interesting dynamic. Also, crossovers that explore the moral and ethical themes from both series are quite popular. Since both series deal with complex ideas about right and wrong, a crossover that delves deeper into these concepts can be very engaging for fans.
Well, perhaps a great plot twist is that Naruto's immortality is actually a curse in the Fairy Tail universe. The magic there has a different set of rules, and his inability to die disrupts the natural balance. This could lead to him being hunted not just by villains but also by some of the more morally strict magic guilds. Also, imagine if Naruto discovers that his past enemies in the Naruto world are somehow connected to an ancient evil in the Fairy Tail world, and he has to fight them again in this new context.
One interesting plot twist could be Sakura having to adapt to Fairy Tail's magic system. Maybe she discovers a new form of her own chakra-based abilities that interact with Fairy Tail magic in unexpected ways. For example, her healing jutsu could combine with Fairy Tail's healing magic to create a super - healing spell.
One interesting plot twist could be when the magic from Fairy Tail interacts with the sins' powers in Nanatsu no Taizai. For example, if Natsu's fire magic somehow combines with Meliodas' full counter, creating a new and unexpected power. Another could be the characters being transported to the opposite universe and having to adapt. Like Lucy ending up in Britannia and having to deal with the Holy Knights while the Seven Deadly Sins end up in Fiore and face off against the dark guilds.