Well, 'Pokémon Reborn' has an amazing story too. It presents a post - apocalyptic world where the region has been destroyed by natural disasters. The Pokémon are often mutated and the environment is harsh. The protagonist has to not only battle other trainers but also deal with the challenges of this ruined world. There are moral dilemmas in the story, like whether to trust certain characters who seem to have their own agendas in this desolate place.
In 'Pokémon Uranium', the story is also great. It's set in a new region called Tandor. There are new Pokémon species to discover. The story focuses on a scientific experiment gone wrong that leads to dangerous Pokémon and situations. The main character has to find a way to fix the problems caused by this experiment while also competing in the Pokémon League. It's a story that combines adventure, mystery, and the classic Pokémon battling elements.
One of the best Pokémon fan game stories is in 'Pokémon Insurgence'. It has a really engaging plot where the world is in chaos due to the Delta Pokémon. The main character has to rise up against an evil cult that wants to use these powerful and different Pokémon for their own dark purposes. The story is filled with twists and turns, like the discovery of the true nature of the Delta Pokémon and the hidden motives of the cult leaders.