I think Sins has great background stories for each faction, but they are not incorporated into the actual gameplay.
Single-player campaigns as seen in Starcraft and many other RTS are hard to implement, as the tech-trees are not meant to be unlocked tier for tier and one game is a whole war instead of a single battle.
What I would really like to see, are story-elements triggered by certain events as seen in Sid Meier's Alpha Centauri. As a classic 4X-TBS game, it's gameplay is quite similar to Sins, so it'stechnique to convey a story should work for Sins too. In Alpha Centauri, certain events as the development of key technologies, the first won/lost battle or the first attack of alien lifeforms triggers an interlude about your reaction towards this events.
You discover a technology that enables you to breed and weaponize the native lifeforms and in the interlude you entrust your second in command with the first new troops.
If you then loose this troops in battle against another faction, you get an interlude, describing how you are presented with the burned corpse of your second in command, shattering your hopes of grooming him as your heir.
After you claim the first city of that enemy faction, you rename the city in honor of your fallen friend.
In this way it would be possible to take otherwise insignificant events from a normal single-player game and make the defeat/victory more personal. After all, the simple message that you lost a planet doesn't really convey the horror of an orbital nuclear bombardement of a whole world. This could either be done in form of a written story (as in Alpha Centauri) or in form of little cinematics (maybe similar in style to the original Sins intro).
So, what do you think of this idea?