There could also be some new characters introduced in this fanfiction. Maybe a mysterious figure who has the power to control Dark Sonic or someone who has a connection to the origin of Dark Sonic. These new characters can bring fresh plot twists and new relationships to the story.
The interactions can also be based on mutual goals. Say there's a threat to both Sonic's world and Equestria. Sonic and the ponies would have to communicate and combine their strengths. Sonic could use his speed to scout ahead and the ponies could use their magic to hold off enemies. They might also share their knowledge with each other. Sonic could teach the ponies about technology from his world, and the ponies could teach Sonic about the magic spells and potions that exist in Equestria.
Sonic, of course, is a must - have. But also Knuckles from both universes. In Sonic Boom, Knuckles is a bit more of a muscle - brained character in a fun way, while the classic Knuckles is more serious about guarding the Master Emerald. When they meet, there could be some hilarious misunderstandings at first, like Sonic Boom Knuckles trying to show off his strength to the other Knuckles, but then they end up teaming up against a common threat.
Well, Sonic himself is often really popular in fanfics. He's the main character of the franchise after all. His speed and adventurous spirit make him a great centerpiece for many stories. Writers can easily create exciting plots around his adventures, battles against Eggman, and his relationships with other characters.
One common theme is friendship. Sonic, Tails, Knuckles, and the other characters have such strong bonds, and fanfics often explore these relationships further. For example, how they support each other during tough battles or when facing personal problems.
Amy Rose can also be a main character. She has a huge crush on Sonic and often chases after him. In fanfiction, she might be involved in more complex relationships with Sonic and other characters, adding an interesting dynamic to the story.
Obviously, Sonic himself is extremely popular. He's the main character, and his speed and heroic nature are often central to the fanfiction plots. Tails is also quite popular. He can provide technical support or be Sonic's sidekick in adventures within the gaming world.
Tails is a very popular character to include. He is Sonic's best friend and his technical skills can add a lot to the story. For example, he could help Sonic and Shadow figure out some complex machinery or technology that is part of the plot.