I'd also imagine a MMORTS would be a viable option. Imagine a persistent MP campaign waging across the whole galaxy, players going at it with each other, and advancing up the ranks if your respective race. Hell, GW could even host their own Fluff tournaments on it.
If we are going to go the way of an MMO, a formula like WoW would probably only work with something like one set on Necromunda, with gangs, cops, rogue traders, cults, etc. Maybe even GorkaMorka. But I find it hard for a warlike sci-fi to be with this kind of formula.
I'd personally like to see an MMOFPS (After DoW II. I'd like to see that first), based on the Planetside formula, WWII Online, or Huxley(if that comes out good).
an MMORPG, in the 40k universe would be very pointless unless its a first-peson shooter (you might be able to find a way to make it an rpg). WoW style combat would be very boring and would not do justice to the intense combat in the 41st millenia.. A shooting game wher its 'choose your move' just doesnt strike my interest, i probably wouldnt buy it.
Like GDICommando said, i have to agree that a level-up/loot first-person shooter rpg in the necramunda environment would probably be best for that.
I just think that in an RTS campain like the sugested, you should be able to choose multiplayer or single player.
I'd like a first person shooter thing, i would like to drive a razor back, or even better, A MONOLITH!