Dr. Eggman could team up with a Pokemon villain like Team Rocket. They could combine their technology and evil plans. Eggman might use Team Rocket's knowledge of Pokemon to capture strong Pokemon and use them in his machines, while Team Rocket could benefit from Eggman's advanced robotics to create more powerful devices for stealing Pokemon.
In a 'sonic meets pokemon fanfic', it could be interesting if the Pokemon themselves gain some of Sonic's abilities. For example, a group of Pikachu learn to run at Sonic - like speeds after being exposed to some chaos energy. This new ability changes the way Pokemon battles work in the region, and Sonic has to help the Pokemon trainers adapt to these changes while also dealing with an antagonist who wants to use this new phenomenon for their own evil purposes.
In a 'sonic meets pokemon fanfiction', Sonic could end up in the Pokemon world and start racing against some of the faster Pokemon like Rapidash. Maybe he'd form an unlikely friendship with Pikachu, with Pikachu using its electric attacks to help Sonic out of tough situations, like zapping robotic enemies that Sonic might encounter in this new world.
One idea could be Sonic and his friends accidentally end up in the Pokemon world. Sonic's speed could be a unique ability in Pokemon battles, like a super - fast attack or a way to quickly dodge enemy moves. For example, he could use his speed to outrun a powerful Pokemon's attack and then counter - attack. His friends like Tails could use his inventions to interact with the Pokemon technology, perhaps creating new Pokeballs or devices.
One possible plot could be Sonic accidentally running into the Pokemon world while chasing Dr. Eggman through a strange portal. He teams up with Pikachu to stop Eggman from stealing all the Pokeballs in a Pokemon center. Sonic's speed and Pikachu's electric attacks would make a great combo against Eggman's robots.
I think Sonic himself would be the most interesting. He's so different from the Pokemon world. His super speed and his attitude would really stand out. He doesn't have the typical powers of a Pokemon, like shooting fire or electricity. His way of dealing with problems, which is mostly running really fast and spinning into things, would be really unique in the Pokemon world.
A possible plot could be that Sonic from Sonic X and Sonic from Sonic Underground meet and initially have a bit of a rivalry over who is the faster or better Sonic. Then they realize they need to work together to stop an evil force that is threatening both their worlds. Another idea is that the characters from Sonic Underground are lost in the world of Sonic X and they have to find their way back home while dealing with the new threats and friends they encounter there.
Friendship is a common theme. Sonic, coming from his own world, has to understand and adapt to the friendship - centered world of MLP. Another theme is adventure, as Sonic's high - energy nature often leads to exciting quests in Equestria.
A common theme is the clash of different worlds. Since Sonic and Pokemon come from different universes, seeing how their worlds collide and interact is often explored. For example, the difference in technology between Sonic's world and the more natural - based Pokemon world.
Another place to find them is on some dedicated Sonic or Pokemon fan forums. Often, fans will share their own fanfics or recommend ones they've read. For example, Sonic fansites might have a section for crossover fanfics where Sonic Pokemon ones could be found.