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.
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.
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.
One idea could be that the Crystal Gems find a strange Pokemon in the woods near Beach City. They initially mistake it for a new type of Gem monster. For example, a Pikachu that has an electric aura similar to the energy the Gems use. The Gems then try to figure out how to deal with this 'creature' which leads to humorous and heartwarming interactions as they learn about Pokemon.
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.
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.
One idea could be that Lars and Steven go on a space adventure together. They might encounter new gem species and have to work together to solve problems. For example, they could find a planet where the gems are in a civil war, and Lars and Steven use their unique skills to bring peace.
In 'jojo x marvel universe fanfiction', the idea of a Joestar character having a crossover with the X - Men is really cool. Maybe a Joestar with a stand that has mutant - like abilities could join the X - Men. It would be fascinating to see how the Joestar family's values and the X - Men's fight for mutant rights would interact.