sounds like you have 3 design criteria:
1. model what a galactic emperor could do with respect to colonization.
2. model independent colonization by private parties.
3. eliminate micromanagement.
an emperor could allocate funds, direct which planets are to be colonized, and award contracts to private sector organizations. they could also send out the military fleet to explore along with come colony ships, colonizing anything they found in the process. they could also direct which sectors of space are to be explored next.
so they set the budget, choose colonization targets, award contracts, can opt to send out the fleet on exploration and colonization missions, and direct where to explore.
i like technogoth's idea of infrastructure points for tracking colony growth. i also like the budget ideas, except perhaps for extra funds going to colony ship construction. to reduce micromanagement, ship construction should probably be on a JIT basis. so the player would say "colonize Tau-Ceti 7", and the game would automatically build the ship and fly it there and establish the colony (assuming funds were available).
for a "hands off" emperor sim, the player has a few basic commodities to work with: money, time, territory, population, resources, and units/buildings.
and the player can issue high level orders: explore here! colonize there! go to war with those guys!
and then the AI takes over.
i've actually been working on a hands off emperor sim myself, City States, with an ancient greek city state type setting.