One way is through fan communities. They can set up guidelines that encourage positive and creative storylines. For example, they can host contests for the best fanfiction that focuses on positive themes like a Pokemon's journey to master a new skill.
Publishers and platforms that host Pokemon fanfiction can also play a role. They can have a strict review process to filter out inappropriate content and promote those stories that are positive, educational, and in line with the spirit of the Pokemon franchise. For example, highlighting fanfictions that explore the unique cultures and habitats of different Pokemon regions.
Educating fans about the impact of their writing is also important. By making them aware that Pokemon has a large and diverse audience including children, they might be more inclined to write positive stories. For instance, writing about how Pokemon teams work together in a rescue mission can be very inspiring.