Well the reason MMO-RTS are so hard to create is that the moment you log of everything pretty much goes down the drain.
No, what I meant is actually an MMORPG where you control one and only one ship (plus fighters if you have a capital ship capable of housing them) and then you live in one of the three empires, who are controlled by AI, and try to affect the outcome.
That way you can engage into the many fleet battles that the AI take part in or make your own raid, deep in enemy territory with some friends. Likewise you may end up fighting other people doing the same thing you are but for the other sides.
I mean how much extra work would it need to make it possible? The GFX engine is really nice so not much improvment needs to be done there and the AI seems quite capable of fighting each other so I imagine the bulk of the work would be to create a server-client architecture where the server holds the state of the persistant world and keep track on the AI.
I for one would think it would be a great game...