One idea could be that Sonic accidentally enters the world of Equestria Girls while chasing Dr. Eggman through a strange portal. He then teams up with the girls to stop Eggman from stealing the magic that powers their world. Another could be a race between Sonic and Rainbow Dash which gets interrupted by a common enemy.
Sunset Shimmer and Sonic might be the first to interact. Sunset has a bit of an edgy side and Sonic is always ready for action. If Sonic showed up in their world, Sunset would probably be the one to confront him, thinking he's a threat. But as Sonic explains his situation, they could start to form an alliance. Also, Sunset has experience with different worlds and magic, which could be useful in helping Sonic navigate the Equestria Girls' world.
Another theme is the clash and then the melding of different cultures. Sonic's world has a more technological and action - based culture, while Equestria Girls has a world full of magic and school - based social structures. Fanfictions often play with how these two different cultures interact. Characters might be initially confused or in conflict due to the differences, but eventually they learn to appreciate and work with each other.
Definitely Twilight Sparkle. In both worlds, she's a key character. In the MLP world, she's a powerful magic user, and in the Equestria Girls world, she can bring her intelligence and her problem - solving skills. Also, Rainbow Dash would be great. Her confidence and athleticism in both forms can create really exciting scenes, like when she races against the Equestria Girls' best athletes or uses her pony flying skills to save someone in a high - rise building situation in the Equestria Girls world.
One common storyline is Sonic getting transported to the Equestria Girls' world and having to adapt to the new environment. He might have to deal with the different magic and social norms there. Another could be Sonic teaming up with the Equestria Girls to fight a common enemy, like a powerful villain from either his world or theirs. And sometimes, there are stories about Sonic teaching the Equestria Girls about his speed and abilities, and in return, they teach him about friendship in their unique way which is very different from what he experiences in his own world.
One interesting story could be about Sonic somehow getting transported to the Equestria Girls' world and having to team up with the girls to stop a new villain. Maybe he uses his speed to outwit the bad guy while the girls use their magic and friendship powers.
Friendship is a big one. Just like in the original My Little Pony series, the idea of different characters coming together and forming bonds is common. Sonic, being from a different universe, has to learn to work with the Equestria Girls.
One popular sonic equestria girls fanfiction might be those that involve crossovers between Sonic characters and the Equestria Girls universe in a friendship - based adventure. For example, stories where Sonic and Rainbow Dash team up to save both their worlds from a common threat.
The main characters are likely to be the Equestria Girls themselves. Twilight Sparkle from the human world would be a central figure as she often takes the lead in many situations. Then there are her friends like Rainbow Dash, Pinkie Pie, etc. Also, the pony versions of these characters might play important roles as they interact with their human counterparts.
Maybe there's a villain from the MLP world that follows them into the Equestria Girls world. The girls then have to team up with their Equestria Girls counterparts to defeat this villain. They could combine their different skills, like the pony Rainbow Dash's speed in the air and the Equestria Girls Rainbow Dash's skills on the track team.