One idea could be that Naruto characters are somehow transported to the FMA world and have to adapt to the rules of alchemy. For example, Naruto might be intrigued by the concept of equivalent exchange and try to apply his ninja way to it. He could learn alchemy and use his chakra in unique ways to manipulate it.
I think Naruto himself would be really interesting. His positive and determined attitude would contrast with the often darker and more complex world of FMA. He could bring his unique brand of ninja spirit and try to make friends with the characters in FMA. His ability to use chakra and his various jutsu would also create some really cool interactions when faced with the alchemists and their powers.
Often, these fanfictions blend the dark and complex world of Fullmetal Alchemist with the idea of 'lust' which could be in terms of a character's desires or a new, alluring force in the story. They might also explore different character relationships and how 'lust' can either strengthen or disrupt them.
One common theme is identity. Since the homunculi are in a new crossover world, they often question who they are and their place in this new setting. For example, in many crossovers, they might compare themselves to the new characters they meet.
Some fma crossovers involve characters from DC Comics. Picture Batman or Superman in the world of FMA, dealing with the concept of equivalent exchange and the political intrigue in that world. It can lead to some really unique storylines and character interactions.
One great fma scar crossover fanfiction could be where Scar teams up with a character from another universe to fight a common enemy. For example, a crossover with a character from Naruto. Scar's unique alchemy skills combined with the ninja's jutsu would make for an exciting plot.
A lesser - known but very creative fma envy crossover fanfiction is the one that combines the world of FMA with a steampunk - themed universe. Envy has to adapt to the new rules and technology in this world, and the story does an excellent job of showing this transformation.
First, know both universes well. For an fma crossover, you need to understand the rules of alchemy in FMA and the characteristics of the other universe you're crossing it with. For example, if it's a Star Wars crossover, know about the Force and lightsabers as well as alchemy.
Another theme is the combination of powers. How can the chakra system from Naruto and the alchemy in FMA work together? Writers often explore this by creating hybrid powers for the characters. They might give a character the ability to use alchemy to enhance their ninja abilities or use chakra to fuel alchemical reactions, which makes for some really creative and exciting storylines.
First, know the characters well. Understand Greed's personality, his desires, and his powers in FMA. Then, research the other fandom you want to crossover with. Next, create a unique and engaging plot that combines elements from both worlds in a seamless way. For example, if it's a crossover with a fantasy world, think about how Greed's alchemical nature would interact with magic. Don't forget to develop good character relationships and let the story flow naturally.