Well now that Entrenchment is out. I'm sure you'll all want to take a bit of time off before starting the next extension, but I figured I'd like to get started on what I would like to see:
Leaders.
Governors would be in command of a planet, they would affect a planet and all structures behavior in it's well except for Starbases (they wouldn't affect ship performance). Governors might have bad or good traits, and you could replace them, but there would be some issues related to replacing a governor. Under some conditions, the governor might rebel, creating either a neutral planet, or even a new pirate base. Additionally, replacing a governor would be expensive, and they would be replaced with a randomly generated governor. Governors could be transfered between planets, but you would actually need to use a capital ship to do so (anything else is beneath their dignity) carrying the governor from the origin planet to the target planet.
eg, some Governors might give the planet they're in charge of a benefit to trade, others might be retired spacers, and their knowledge would give allied ships speed benefits, others might give defensive or offensive benefits, others might make research happen faster, or their planets develop more culture, etc.
Loss of a planet would result in loss of a governor.(ie he gets killed) They might be bribeable if espionage is improved.
Officers would command ships, Officers would also be able to have both good and or bad traits. Officers would gain levels based on combat much like ships do, and they would be capable of influencing the ship(s) under their command with those traits, sometimes even granting special abilities. Officers could be replaced, or promoted. Promoting and officer would cost resources and or money, it would give them a level, and they could be transferred to another ship. Officers that are replaced rather than promoted (eg in order to remove a bad officer) would have a possibility of rebeling and attacking you or joinging a pirate or enemy faction, along with their ship. If an officer is promoted they would need to be moved to a higher end ship (eg an officer in command of a Frigate would have to command a Cruiser after promoted, if promoted again they would need to command a Capital ship or Star Base. If promoted again, they would need to command a Flag Ship or Academy. Most officers would be trait neutral (ie have no outstanding traits) Trait Neutral officers would effectively not show up, they wouldn't affect ship performance.
Potential skills might be space knowledge, the officer knows of an invisible wormhole or space lane that knowone else knows of, or ships under his command may move faster.
Officers may have several traits, sometimes good, sometimes bad, all affected by the presence of an academy.
A new structure called an Academy would give you a better chance of developing officers with good rather than be skills (affected by research) Officers sould also command Star Bases. An academy would be about as expensive to build as a Star Base, have similiar firepower, but similiar resilience, and you could only build ONE per race. (not one per gravity well) They would be REALLY frikkin' expensive (much more than a Star Base) Blowing one up would be a major event. You COULD build a Star Base in the same well as an Academy. Building an academy at the Capital of the Empire would be cheaper than elsewhere,
You could do research that would increase the likelihood of specific trats developing amongst officers (researching some traits might close off other research corridors however)Flag Ships would something you could choose and put in control of a fleet, the officer in charge of a Flag ship would confer his skills not just on the performance of his ship, but the entire fleet. Flag ships would also get an experience bonus (only for themselves) Officers would be more likely to gain levels when in command of larger or more important ships (as well as survive) Each tiem you create a ship, an officer may or may not be created (again affected by the presence of an academy and the type of ship).