Silly question: is it possible to give units different missile loadouts and special abilities according to faction, as has been done with fighter loadouts?
It just hit me that Maldrood, with its tendency to raid with VSDs in Darksaber, could be the "fast" faction, with increase firepower being replaced with power to engines for any ships with the former ability (useful when trying to retreat a VSD), and Zsinj's VSD Is might have some anti-fighter missiles as part of the loadout (one VSD does one-shot a shuttle in the Courtship of Princess Leia), with Zsinj being potentially an "anti-fighter" faction.
Eriadu might have longer-ranged, weaker missiles as I suggested before, but with VSDs and bombers having such a change.
Just some thoughts. I'm only suggesting this if it adds a little more flavour with little work required. I do not want to suggest something that requires tons of work, given that you've done so much already. Just ways to make certain ships different to the same class under a different faction.