Right, it would work best, and be most ideal, if everybody started out on equal footing. But it's impossible to say that cross game importing wouldn't work.
MMOs inherently function differently to single player games. They demand a unique, multiplayer focused environment with carrot-on-a-stick design to keep members actively paying/subscribing. A good MMO ('good' as in 'hooks consumers') will use instancing, scaling and other features to make players feel there's always something to aspire to.
If it were simply the handheld games made massive multiplayer, it wouldn't work. It wouldn't work as a ground up MMO either. The entire construct of what is a Pokemon game would need an overhaul to take into account long term play with thousands of players interacting with one another.
But it still could be done with imports. What you need is game mechanism that shape to player skill level, so that import still have something to work towards.
Pokemon is inherently an OCD collect-a-thon by design. You could easily rope in dumb grinding features, rewards and other junk that would keep people playing, even with the same Pokemon that they always use.
Yeah, but this is typically dumb, backwards thinking shared by many Japanese developers/directors and why the country is falling so far behind the West in terms of digital distribution and community driven networking.