A cool concept could be a possession story. A powerful supernatural entity tries to possess members of both groups. Scooby Doo and the Mystery Skulls have to find a way to stop it before it's too late. This would bring out different reactions from the characters. Scooby and Shaggy might be more panicked, while the Mystery Skulls, with their prior experience, would be more strategic in their approach.
Vivi and Velma would make an interesting pairing. Vivi has her own knowledge of the supernatural world, and Velma is the brains of the Scooby Doo gang. They could share their insights and research methods, and Vivi might introduce Velma to some new concepts in the supernatural realm that Velma has never considered before.
A Scooby Doo and Harry Potter crossover fanfic would be cool. The gang could go to Hogwarts for a school trip and end up having to solve a mystery involving a poltergeist that's scaring students. They'd have to use both their detective skills and some magic knowledge they pick up along the way. Shaggy and Scooby would probably be really excited about all the food in the Great Hall.
Well, perhaps there could be a crossover where Scooby and Shaggy accidentally eat some magic cupcakes in Equestria that give them the ability to talk to the ponies in a special way. Then they discover that there is a mystery surrounding a disappearing magical element in Equestria. The rest of the Mystery Inc. gang shows up to help, and they all join forces with the ponies like Rainbow Dash and Fluttershy to find out what's going on and save the day.
One idea could be that the Winchester brothers are hunting a ghost in a town where the Mystery Machine gang also happens to be. The Scooby gang initially mistakes the Winchesters for bad guys but then realizes they're all after the same spooky entity. They could team up, with Sam using his research skills and Dean showing the Scooby gang how to handle real weapons (in a non - dangerous way, of course).
One idea could be that the gang discovers a mystery related to an ancient curse in their hometown. Maybe there are strange happenings around an old, abandoned mansion that was once the site of a dark ritual. Another could be a mystery involving a new, mysterious character who seems to know more about the gang's past adventures than they do themselves.
Perhaps a crossover where Scooby and Shaggy end up in a post - apocalyptic world. They have to rely on their survival skills, which they've developed from all their mystery - solving adventures. They could meet new characters who are tough survivors but lack their unique sense of humor and ability to find food in the most unlikely places. Together, they work to uncover the mystery of what caused the apocalypse.
In a fanfiction crossover, Ghost Rider could end up in the Mystery Machine by accident. His flaming skull would surely freak out the gang. However, he might need their help to track down a villain who has escaped into the world that Scooby Doo and his friends inhabit. They could combine their skills, with Ghost Rider's supernatural powers and the gang's mystery - solving abilities.
A really cool concept would be a fusion of the two worlds. For example, the villains from the Naruto world could be using Scooby Doo - like disguises to deceive people in the Hidden Leaf. It could be Orochimaru in a mummy costume or something. Naruto and his friends would have to use their ninja skills and also learn from the Mystery Inc. how to unmask the villains by looking for clues.
One interesting aspect is the character interactions. For example, when Scooby Doo and his gang cross over with characters from other shows, we get to see how their personalities clash or complement each other. It can be really funny to see the cowardly Scooby interact with a very brave character from another series.
One idea could be that the Kiss band members team up with Scooby and the gang to solve a mystery at a spooky concert venue. The strange happenings could be related to a cursed instrument that causes supernatural events.