I saw some1 mention using another channel, that could work. create a lawless channel where anything goes, no storyline. some1 also mentioned EVE online as an example, it shouldn't be hard to implement, though to prevent confusion the channels may need names.
this lawless channel could even spawn guilds and clans, which could replace the NPCs in the game, gyms, villains(team rocket, magma, aqua, galactic, plasma, contoso) elite 4 etc. to make battles fair nerf the guilds Pokémon based on the challengers Pokémon.
you would essentially create a complete MMO experience