Core exiles is the closest we have though it's not exactly empire building although there are many different activities, installations etc (I really ought to get back to the game actually). but I'd love something single player myself where you explore a generated universe and aren't quite as based on bashing other players.
Echo quadrant is a great try at something like this, though I am not sure how far it is able to go as yet, still we'll see, maybe wastelander could create an sf version of warsim next .
With our dreaming and singing, Ceaseless and sorrowless we! The glory about us clinging Of the glorious futures we see,
Our souls with high music ringing; O men! It must ever be
That we dwell in our dreaming and singing, A little apart from ye. (Arthur O'Shaughnessy 1873.)