A great plot could involve a time - travel aspect. The protagonist is sent back to the time when Pokemon Yellow was first set, and they have to use their knowledge of modern Pokemon training and battling to change the course of history in the Pokemon world. They might also meet the original trainers from the game in a different way and form new alliances.
Another plot idea is a story centered around a Pikachu that refuses to evolve. It has its own reasons for not wanting to become a Raichu, perhaps it has a special bond with a certain type of Pokemon that can only be maintained as a Pikachu. The main character has to support the Pikachu in its decision while facing opposition from other trainers who think evolution is always the best path.
Perhaps a fanfiction where the main character discovers a time - traveling device in the Pokemon world. They travel back to the very beginning of the Pokemon Red and Yellow era and have to prevent an event that would change the future of the Pokemon world in a bad way. Along the way, they meet the original Professor Oak as a young man and help him with his early Pokemon research.
One idea could be a story where the main character discovers a new, rare Pokemon in an unexpected place, like in a hidden cave in Viridian Forest. Another could be a fanfiction where the Pokemon trainers from Red and Yellow team up to face a new, powerful villain who has a unique ability to control Pokemon in a different way than the usual villains in the games. Maybe also a story about a trainer's Pokemon evolving in a very different way due to some strange phenomenon in the Kanto region.
One idea could be to focus on a new trainer's journey in the world of Pokemon Yellow. They could start with a Pikachu that has a unique ability not found in the original game.
A cool plot could be that Lance, in the Pokemon Yellow world, decides to start a new type of Pokemon training school. He recruits the protagonist from the game as his first student. Together, they develop new training techniques and discover new Pokemon evolutions. But an old rival of Lance hears about this and tries to sabotage their efforts. So they have to not only deal with the challenges of training and discovery but also fend off this rival who is jealous of Lance's new project.
One idea could be a story where the main character is a Pokemon trainer who discovers a rare and powerful Pokemon that no one has ever seen before. They then have to protect it from evil organizations who want to use it for their own gain.
One idea could be the main character being reborn as a Pikachu and having to navigate the world with its electric powers while making friends with other pokemon. Another could be being reborn as a Eevee and having the unique ability to evolve into any form at will, which causes both envy and admiration among other pokemon. Maybe the reborn pokemon has memories of being a human and uses that knowledge to outwit trainers and other threats.
One idea could be a story where Peridot tries to prove her worth to Yellow Diamond in a non - traditional way. Maybe she discovers a new form of energy on Earth that could benefit the Diamond Authority, and she has to convince Yellow Diamond to give her a chance to explore it further.
One idea could be exploring an alternate timeline where the main character makes different choices. For example, choosing a different starter Pokemon and how that changes their entire journey. Another could be focusing on the backstories of the Gym Leaders in the Pokemon Gold game, like what led them to become Gym Leaders.
One idea could be a crossover where Pokemon trainers visit the Avatar world. They could learn bending techniques and use their Pokemon in unique ways to help the Avatar in a great battle. For example, a Pikachu could use its electricity to enhance a waterbender's attack.
One idea could be a trainer who discovers a rare and powerful Pokemon that many others want to trade for. He has to decide whether to part with it for a large collection of other Pokemon or keep it for his own journey. Another could be two rival trainers who end up having to trade in order to complete a special quest that requires them to have each other's signature Pokemon.