Yes, I definately think something new needs to be thought up here. Blight is old news and doesn't need to be carried from planet to planet, so they can destroy every one they colonize. Nor do they need the blight as continued reason to get them off their butts and go colonize another planet. Colonies splitting up and starting a war seems a little over used too. But hey, I guess it may be human nature or something. Aliens? Yeah, sounds a little far fetched. Does there even need to be the same focus on combat? The aspect of combat does seem to add interest to the game, but I've sorta felt in the past that combat was tacked onto OP2, and I often enjoyed the sim city building like aspect of the game more.
Oh, and that whole savant/blight combo stuff just doesn't do it for me at all. I'd rather see some crazy rogue scientist keeping samples of the blight around that, naturally, gets loose on the colony. But, if this story is of the other ship launched from Earth, that just doesn't work.
So yeah, I'm dying to see what you guys have got for a story, because anything I think about, well I just can't seem to see how I'd ever turn it into a good story. But hey, I suck at writing. That's probably got more to do with it than anything else.