Story/Campaign mode: Added with each expansion? With new races/ships/etc...? With new opening animations? Example
In next expansion it tells of how the TEC have suffered a horrendous loss at the hands not only of the invading Vasari, but also with the second front against the exiled Advent, and have been marginalized to the outer rim worlds. The Advent dominate and are mainly contested by the Vasari. We could now bring in the "unknown" threat that was chasing the Vasari which causes the Vasari, Advent and Tec to unite in a new Coalition against this unknown and very very powerful force.
In expansion two, the Advent and Tec could have been almost completely wiped out, with only remnant numbers and have another race or two races come in to fill those places. Perhaps, the Advent and Tec are slaved races to the OverLords? With the Vasari still running? In this way, perhaps the focus moves away from full blown hundred ship fleet battles, to one or two or three ships running guns or exiles out of the center core worlds to the outer rims? In this way the game style for small ship squads and storylines can be added and played for those that enjoy this (and I am one of them) 
Expansion 3? It has been 4 thousand years since the enslavement of the Advent and Tec races. Even the Vasari are only a memory. There is now only the OverLords and the Common men who man the ships the Overlords control. And Suddenly the Overlords start dying and ship fleets all across the galaxy are left control less. Into this void the World Unions emerge, promising everything and anything to anyone to sign on and pilot or passenger a ship for them. Good wages and fantastic opportunities, in a now lawless galaxy.
Anyway... I'm not a writer, but I was rather impressed with the HW story, and wanted to try to think of something that like that story, incorporated change and time and the flowing of success and failure over that expanse of time.
Story mode is a really really cool idea, tell the devs it is very very important we get it.
and maybe we will. 
my two cents -
-teal