cool we might want to make a quest form. cause the other planets would be more of a quest at first that unlocks them.I'm thinking it would require you to help the guy with his research on dark energy which existed in every area but it would be much easier to research in the shadow world or get materials that can reproduce it easier from the shadow world. Then the guy makes a warp drive engine using it. much like how nasa is trying to develop our warp drive using dark energy. XD
heres some ideas on how it could work
mods could work in several ways, as new campaigns that are a whole new set of maps with possibly new pokemon etc that have their own 'game type' that can't trade/battle/coop with players of the base game. these are basically pokemon 3d 'rom hacks'.
as a small collection of maps you can load into from the main game (these would probably need to be approved case by case to see if they can be playable on peoples normal characters without breaking the game). these mods could have different level ranges so they are alternate quests you can go on at various points in the game. these mods would not have new pokemon and would have to not be overgenerous with items etc
and finally as small things like letting people swap sprites clientside etc, kind of like your typical bethesda RPG game cosmetic mod. funny moustaches on all the trainers, play as trainer red, metal suit for your mewtwo. other players you coop'd with would just see the defaults unless they had mods.
the key thing with mod support is keeping them separate and safe, while ensuring that your own files don't get tampered with for cheating etc.
For now, without this kind of support I reckon you could do mod loading via save games, you package a save with your mod and players can change the name and skin (make it part of the installation process if you wanna be fancy) and if they load the save it'd load them into your entry map, so you don't have to mess with the official maps at all, like i did with my route 69 test map