Looks promising. I believe that Blizzard's StarCraft, and to an extent WarCraft III has proven that gamers can easily handle games without a 'happy ending'. In fact, in the Frozen Throne expansion, you're actually striving to see (one of the) bad guys win in the end. I guess it all depends on the wrapping in which the game and story in presented.
I, for one, am curious has the Terran will have evolved in that pocket universe and on Earth. I could imagine them gradually turning darker over time. After all, they 'lost' their homeworld in part due to the incompetence of their allies (their words) and the maniacal Drengin and Dread Lords. So, when they come back, everyone is going to pay.
At least, that just my little fantasy. I think humans could make very good evil guys, after all, a human mind unrestrained by ethics to outsiders can be a fearful weapon. And their loyalty towards one another would create a solid block of an empire.
Oh well, that's the story I often pretend to be playing in the game.