I love this game. I find it mesmerizing. Just a couple of things would make it even better:
The pool of available ships includes not just ship types, but individual ships.
Have a “captain management system” in which captains of starships have certain characteristics (such as fatigue, morale, etc.) and abilities (tactical skill, command and control, inspiration, etc.) that are affected by battle experience. (I’m thinking about something like Matrix Games’ “Hornet Leader” and the like that model pilot’s states.) This would provide a sense of attachment to individual ships, thus affecting deployment of vessels.
A simple strategic overlay. I am thinking of the old DOS Star Trek game, where you are presented with a map of the universe, divided into quadrants. You would move the Enterprise from quadrant to quadrant, battling whatever Klingons were there and taking repairs at space stations. For GSB, we could have the same thing, only with the ability to create and move fleets about. The goal would be to clean out all the quadrants of the enemy fleets. With random placement of enemy fleets, and random elements included in the quadrants, this simple strategic overlay would be endlessly replayable, and would break the game out of a rigid mission tree.
Above all, keep to the original concepts that make the game great: the vast customization options, the simple “grand view” military only approach to tactics and strategy (please don’t turn the game into a 4X space opera), fantastic 2D graphics that never devolve into textured polygons and that allow us to enjoy cinematic action without forcing us to drive a camera around.