Damn, my previous post with lots more detail didn't get posted for some reason, so here's the short-short version of things that would be awesome:
1) Unique racial bonuses (similar to MOO or Space Empires). Populations of races are already track. Simple implementation would be to provide planetary bonuses only, advanced implementation would allow ship crew populations to be tracked to provide bonuses to ship systems (think star trek) and ultimate implementation would allow different leaders of different races to provide different kinds of bonuses, as well as bizarre bonuses like "doesn't need food" or whatever (think the silicone lifeforms from MOO that consume metals instead of food).
2) Procedually generated leader backstories. Based on their traits & rank, would fill in their history with fluff stuff. Childhood, what kind of education they had, for officers it would "back-date" when they were promoted through the ranks.
3) Morale for ship combat - low morale ships might break and flee combat, high morale ships might start ignoring orders, charging into combat. Simple would just have it happen within the battle itself, advanced implementation might have the ships deviate dramatically, possibly even jumping to get back to the nearest friendly ship (or to attack the nearest hostile ship). Complex implementatoin might have the ship go rogue if extreme morale happens and become AI controlled (not NPR, would wander around like a pirate seizing goods!)
4)Expand Leader Skills - more skills are always more welcome. Situational bonuses like +10% offense or +10% defence, Ambush (+% damage when enemy isn't/can't target back), Longshot (+% to hit at >1/2 range), Weapon Specialties (+% to beam weapons). Those could be even further subdivided, so a defensive expert might have bonuses to armor resistence or shield resistence or shield regeneration.
5) Heart of Iron III style "waterfall" bonuses. Basically for ground units, you set up traditional tiers (Brigade -> Division -> Corps -> Army). Basically an Army commander would have X Corps under him, which each have Y Divisions which each have Z brigades. This would be a formal organization that the player would set up. The bonuses of the higher ranks filter down at a highly reduced rate, so while a Division adds 100% of his bonus to the troop he directly commands, maybe only 50% of that bonus filters down to the Brigades under his command. (arbitrary numbers, tweaking would be necessary)