Make it so new colonies don't automatically listen to you. Every time you expand to a new planet, you have to upgrade a "bureaucracy" building in your capital. Otherwise you have no control over what the new colony does. The upgrade and upkeep costs of your "bureaucracy building" scales exponentially so if you want to micromanage you're going to have to pay with in-game currency.
Colonies with large population can become capitals, too, meaning that the player is encouraged to build up the population of new colonies so they can avoid the problem of exponentially more expensive bureaucracy upgrades.
Point is: bureaucracy can be fun. Some people enjoy it. But keep it optional. For the players who don't want to micromanage, and are ok with the AI handling things, they don't have to build the bureaucratic buildings.
