Dun Morogh, Elwynn Forest, Durotar, etc. in WoW; Limsa Lominsa, Gridania, and Ul’dah in FFXIV--in every MMO there always needs to be a starting area. So what, pray tell, would be the starting areas in a Poke-mmo? It’s a good thing there are already predefined and segmented regions of the Pokemon Universe. Players would be able to pick from the Kanto, Johto, Hoenn, and Sinnoh regions; they'd be confined to their respective region, and the Pokemon in it, until they are high enough level to venture out.
This game pretty much designs itself, since the gym leaders already exist as level stop-gaps in the games. Defeating gym leaders would be a quest that continually opens more and more areas of the region, until you defeat a gym leader that let’s you fly to other regions. Beating the Elite Four unlocks the end game in that particular region. And, of course, catching your first Pokemon would be your first quest.