A thunk just hit me, ladies gentlemen and gelatenous blobs.
If you can form fleets, why not hire a commanding officer? He could impart serious bonuses in certain areas, like a colony fleet gets a range boost or a battle fleet recieves + attack and defense. Second idea: a flagship could be chosen for this officer, and it it's taken out the officer dies and the bonuses turn into penalties for the ships.
Second idea: Civilization Flagship. Not like the survey ship, I'm talking a hull size beyond Huge, a massive behemoth that costs no logistics and thusly can join your forces easily. But you only get one every set of techs [early game would give a survey ship, once you have basic weapons you get a warship instead] and if it's destroyed you get severe combat penalties.
Just a thought.
