One possibility is that they would compare their Pokedex collections. Each protagonist has had unique adventures and caught different Pokemon, so they could show off their rarest finds and share stories about how they caught them.
It could be the newer protagonists who are more surprised. For instance, if a protagonist from a more recent game meets Ash, who is like a legend in the Pokemon world. They would be in awe of his adventures and his reputation, while Ash might be more used to strange encounters compared to them.
One common theme is friendship. Just like in the original series of both Digimon and Pokemon, the fanfics often focus on how the characters from different worlds can become friends. For example, a Digimon might help a Pokemon in a tough situation and they form a bond.
One common theme is the exploration of different worlds. Since Pokémon and Digimon come from different fictional universes, fanfics often focus on characters from one world exploring the other. Another theme is friendship. The idea of Pokémon and Digimon becoming friends or allies despite their differences is quite popular.
Waves After Waves was a cartoon, and the couple in it didn't exist in real life. Mr. and Mrs. Baiyun were fictional characters in cartoons, and they were villains in Waves After Waves. Their stories were very exciting in cartoons, but they did not exist in real life.
One possible plot could be that the ponies from MLP accidentally enter the Pokemon world. They are confused at first but then start to make friends with the Pokemon. The ponies might use their unique abilities like magic to help the Pokemon in some situations, and in return, the Pokemon show them the wonders of their world.
Another possibility for main characters could be Rainbow Dash from MLP and Blastoise from Pokemon. Rainbow Dash is brave and loves adventures, which would be perfect for exploring the new Pokemon world. Blastoise is strong and reliable. They could form a great team, with Rainbow Dash using her speed to scout ahead and Blastoise using its water attacks to protect them from danger.
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.
Obviously, Ash and Red are the main characters. Ash is the well - known protagonist from the Pokemon anime series, and Red is a famous character from the Pokemon games.