A cool concept would be a fanfiction where the villains from both universes team up. The Diamonds from Steven Universe and Dio from JoJo could form an alliance. The heroes from both sides, like the Crystal Gems and the Joestar family, would then have to put aside their differences and work together to defeat this powerful and unexpected union of evil.
Maybe a story where Steven, being his empathetic self, tries to understand the complex and often morally grey world of JoJo. He could meet Jotaro and learn about Stands. In turn, Jotaro could be intrigued by the Gems and their unique way of life. This could lead to a series of adventures as they try to find common ground between their two very different worlds.
One idea could be that Ichigo from Bleach ends up in the Steven Universe world. He might be confused by the Gems' powers at first. Then he could learn from them and they from him. For example, he could teach the Crystal Gems about his Hollow powers, and in return, they could show him how to use Gem magic in a new way.
Perhaps in the fanfiction, there is a threat that only the combined forces of the Naruto universe and the Steven Universe can stop. Naruto and his friends team up with Steven, Garnet, Amethyst, and Pearl. They have to learn to work together, with Naruto's combat skills and the Gems' unique abilities being essential in defeating the common enemy.
I think a pairing between Pearl and Giorno would be really interesting. Pearl's grace and combat skills, along with her loyalty, could pair well with Giorno's determination and his ability to create life with Gold Experience. They could have some really cool fight scenes together against common enemies.
Perhaps Steven finds himself in a situation where he has to protect a number of characters, and in the process, they all fall for him. Like he could be on a mission to save some of the corrupted Gems, and as he heals them, they see his pure intentions and are drawn to him. This could lead to a harem where they all vie for his attention in different ways, some being more shy and others more bold in their affections.
One idea could be that the OC is a new gem who arrives on Earth and Lapis is initially suspicious but gradually warms up to them as they show their kind nature. For example, the OC might help Lapis with her water powers, like finding new ways to control and shape water in a more creative way.
A possible plot is that Naruto and Steven are summoned to a world where a prophecy states they will form a harem to bring balance. Each member of the harem has a special role or power related to either Naruto's world of ninjas or Steven's gem world. As they interact, there are comical misunderstandings due to their different backgrounds, but they gradually form deep bonds and work towards fulfilling the prophecy.
One idea could be that Steven tries to understand Blue Diamond's past traumas and helps her heal. Maybe he uses his unique powers of empathy to break through her cold exterior.
One idea could be that the reader is a new gem on Earth and Spinel is initially suspicious but then they become friends through exploring human culture together. For example, they could go to a carnival and Spinel discovers the joy of cotton candy.
Another possibility is a crossover with "Gravity Falls". Dipper and Mabel could come to Beach City during a mystery involving Gem technology. Their knowledge of the strange and unusual from Gravity Falls could combine with Steven's understanding of Gem lore to solve the mystery.
One idea could be that as a girl, Steven has different relationships with the other Crystal Gems. Maybe she forms a really close sister - like bond with Pearl, who becomes overprotective. Another could be that her fusion forms take on a more feminine aesthetic and she has unique experiences when fusing with the others.