I was doing some thinking on this:
At the end of the campaign the player flagship becomes extremely powerful. With the right modifications you can trivialize any battle. Without heavy nerfs, the endgame combat power of the flagship will make it difficult to create challenging encounters in new DLC.
So here is an idea:
At some point, future DLC begins a second story with a new captain -this time commanding a Lexite starship that is trying to return to Earth from a distant galaxy. This allows the players to start over in a new sector of the galaxy with a second starship to upgrade.
Perhaps after wrapping up the main plot of the Lexites, the Humans and Lexite stories join together -allowing the player to choose which flagship to use as their main.