One thing about Mystery Dungeon Red/Blue - some of the friend habitats (a weird system in itself) show clear signs of former human occupation; in particular the Power Plant and Weird Laboratory even mention specifically that they were constructed in ancient times by humans, and then abandoned (creepily, these facilities are still mutely active and executing some eternal autorun). In addition, the pokemon of this world know what humans are but have never met one, as though they were a legend or relic out of the past. Could this world be the same as the one depicted in the other games, just centuries in the future, after some catastrophe induced human extinction - based on the condition of their remaining sites, perhaps a virus (Deoxys???) or neutron bomb? Is the human PC not only altered physically and mentally but also wildly displaced in time? This would also explain the presence in this world of pokemon who could not exist without the intervention of human science, such as Porygon and the otherwise long-extinct fossil pokemon.