Righto. A 40K MMO = ~Awesome. However, holding off on gameplay/mechanisms etc, it's true value will depend on fleshing out the playable races. This is paramount. The races have well established lores/backgrounds and various traits that set them apart from each other; realising them will offer players the most fun.
Personally I'm a soldier of the Imperium, and a seer of the Eldar.
The Imperium, as corrupt, stagnant and decayed as it is by it's bloody history and hindered by it's superstition and misled religion, still possesses some of the choicest characters and factions. The Emporer also constanltly stops the Warp from overflowing into the realm of Reality, so by default all races barring Chaos are kinda in his debt. That can't rub off too well.
Space Marines: While there has been a testorone buildup, in the last few years of gaming especially, of over-armored, stone jawed, Schwarzenegger cut-outs, the Adeptus Astartes are wicked. Blood Angels first and foremost (personally), with other chapters earning well deserved recognition. Being able to choose which Chapter you belong to is important. Very much so.
The Guard have some cool chaps too, but what gets me are characters like Ciaphis Cain, and Gaunt. If you haven't read the novels about these two, I recommend them.
Lastly, what about the [Spanish] Inquisition? How awesome would it be to create your character like Eisenhorn of Ravenor? That should lead to some mean quests.
But the Eldar are just cool. Excuse my fondness of elegance and pointy ears for all elf-haters out there, but coming from the Asrai in Warhammer Fantasy, Eldar are choice. Plus they invented the Webway, and their near-accidental racial suicide led to the creation of one of the four Ruinous Powers. Cool background/character motivation.
For every other race, it'd be shit-sticks cool to be a Necron, Kroot or Tau, Ork, Tyrnaid (esp. fun, if they had similar abilities/gameplay to what the latest version of AvP had to offer) etc. Racial diversity is good. But if they can take that further with factions, classes, belief systems (potentially cool: the Puritan vs Radicals of the Inquisition) etc, that's an enormous boon. And we're always on the lookout for enormous boons, aren't we.