One possibly interesting change to the game would be to revamp the government system to be based on sliders as oppossed to defined government types. Something similar to the system in Europa universalis 2 comes to mind.
So for example, you would have sliders relating to freedom of citizens (ranging from slave of emporer, to standard freedoms, to anarcists) and a slider for individual world freedom (ranging from colony, through local government, to independent worlds). Researching certain technologies moves the sliders 1 point in certain directions (so researching slave pits would move the citizen slider 1 point towards slave). Decisions in occasional pop-ups would also allow the shifting of sliders (eg. a random events). the position of the sliders will determine the exact bonus the player gets from the government. Multiple sliders can all effect the same bonuses.
This sort of system allows the player themselves to either fine tune themselves or allows their actions and decisions to shape the government they desire. Do you grant that planet more independence (+10% cultural resistance, -10% tax) or tighten the reigns of control (+10% rebellion chance, -10% cultural resistance, +20% tax)?
Multiple sliders can be added to any aspect of the empire direction that you desire (slider for foreign relations, slider for trade/economics, slider for research/idea control).
Paul.