First, know the characters well from both universes. For Steven Universe, understand the powers and personalities of the Crystal Gems and Steven. For Transformers, know the Autobots and Decepticons. Then, find a good starting point for the crossover, like an unexpected encounter. Don't forget to keep the tone consistent with both franchises.
It could be really cool. Imagine Steven's gem powers interacting with the Transformers' technology. Maybe the Crystal Gems could help the Autobots in some way, like using their powers to repair damaged parts. Or the Transformers could introduce new ways of using energy to the Gems.
One plot idea could be that Markiplier's character is a lost traveler who accidentally lands in the Steven Universe world. He is mistaken for a new type of gem at first. The Gems try to figure out what he is while he is just trying to find a way back home. But as time goes on, he starts to care about the Gems and their cause, and decides to stay and help them against the Diamonds.
A Markiplier and Steven Universe crossover fanfiction could be really interesting. Maybe Markiplier's character could end up in the world of Steven Universe. He could interact with the Crystal Gems, and his comedic and often chaotic personality would create some really fun and unexpected situations. For example, he might try to help Steven with his gem powers in a very unorthodox way that would make everyone laugh.
A crossover could start with Steven somehow getting his hands on a piece of Voltron tech. This could be something that fell through a wormhole. His curious nature would lead him to try and figure out what it is. Meanwhile, the Paladins of Voltron are on a mission to retrieve this tech. When they arrive in Steven's world, they are shocked to find a world full of Gems. The two groups could then learn from each other's powers and ways of fighting.
Another possibility is that a Marvel hero, say Spider - Man, accidentally ends up in Beach City. He teams up with Steven to deal with a local threat that is also related to some sort of interdimensional chaos. For example, a group of villains from the Gem world and the Marvel world are working together to open portals to other dimensions to steal valuable resources. Steven and Spider - Man would have to use their unique abilities to stop them.
Yes, there are likely fanfictions out there that might feature a kiss between Steven and Lapis. The Steven Universe fandom is quite creative, and fans often explore different relationship dynamics in their fan - made stories. However, the official show may not have such a scenario, but fanfiction allows for all kinds of interpretations and romantic pairings that deviate from the main plot.
One interesting storyline could be where Steven's gem powers interact with the magic in the Undertale world. For example, his ability to heal might have a unique effect on the monsters in Undertale. Maybe he could heal some of the more damaged monsters and in turn, they help him understand their world better. Another could be a story where the characters from both universes team up to face a common threat. The Sans and Papyrus from Undertale could join forces with Steven and the Crystal Gems to fight against a powerful enemy that is a threat to both their worlds. It would be really cool to see how their different fighting styles and powers work together.
If it was a crossover with "She - Ra and the Princesses of Power", Adora could be a main character. Her strong leadership and the power of She - Ra would be an interesting contrast to Steven's more laid - back leadership style. Together, they could fight against a common enemy that threatens both their worlds.
One idea could be a crossover with "Adventure Time". Finn and Jake could visit Beach City and interact with the Crystal Gems. They could go on a mission together to stop a new threat that combines the magic of both universes.