I'd like to see a major expansion with more detailed political and socio-economic factors coming into play.
..government choices - all have pros and cons, for any type of victory path
..war exhaustion, even for an attacking race
..laws effecting entire empire, all requiring political credit to implement, have decent bonuses in the direction you want, with slight counter-productive maluses
..cabinet positions - political credit required to change, amount depending on goverment type
..Empire wide morale factor - bonus/malus for numerous scenarios, effects primarily based on government type (losing a planet, troop/citizen deaths, fleet victory/destruction, research accomplishments, expansion, etc)
..disapproval of government can lead to planet flipping to a rival faction or declaration of independence (i.e., become a minor race)
..forced relocation malus (yes, some colonists will want to move to a new planet willingly, but certainly not all - the longer they stay on a planet, the more resistance to move - planetary approval can work in opposite manner with this - higher approval, more resistance to move - lower approval, less resistance)
..government and policies can affect troop conscription rates/costs - a few hundred thousand naval crew is a trivial matter compared with with troops in the BILLIONS
..occupation policies for recently conquered worlds - threat of post-invasion resistance possibly requiring the garrison of troops, etc
Also, much more depth on invasion mechanics, including specialized troop production, garrisons, assault craft tech, etc - I understand that at this point in the game, they wanted to keep things simple, but I just cant wrap my head around the fact that children to florists to the elderly can just be given a gun, and become an effective marine, sending an entire population of a world to another to fight.