A future patch or expansion to GCIII should introduce the concept of sectors or administrative regions to the empire in order to speed up management. Each sector should have a Sector Capital instead of a regular colony capital, granting additional productivity in exchange for greater maintenance (so it would not be viable to spam sectors), and all planets organized into sectors could gain productivity boosts based on their distances from the sector capital (much like shipyards gain production in inverse proportion to distance).
Moreover, sectors could be granted autonomy, given the right to use a percentage of revenue for their own purposes; the granting of the right to revenues would increase morale, and the particular use of the money by the sectors (education, health, agricutlural subsidies, etc.) would increase morale, productivity, population growth, and the like. Techs like Star Republic, Star Democracy, and Star Federation should increase the benefits from such devolution.
These changes would not be terribly difficult to implement and would add significant depth to the game. In future expansion when legislatures/political parties are reintroduced, sectors could also be granted their own legislatures which would implement decisions and have passive bonuses based on the ideology of the party in power.