Your options are either:
1. Command economy. You can micromanage everything on a planet to planet basis.
2. Free market economy. Where you micromanage NOTHING and let planets develop as they wish according to the planetary governors. You can set guidelines as to focus more on research or money or production, but the planetary governors will only follow your guidelines only as much as it benefits their OWN SELF INTEREST (I'm sure there are ways to program this).
However, if you choose the free market path you get MASSIVE economic bonuses everywhere because everyone is happier without some overlord watching over everything they do.
To make this work, get rid of adjacency bonuses totally or nerf them down to 1%. Otherwise Command Economy would still beat Free market economy.
If you set up a Free Market Economy, a large challenge of the game should be you (as the president) trying to get your democratic government to do what you want them to do and sucking up to them and building planetary propaganda centers like Fox News (so you can influence the press) so they'll listen to you.
Example: You (as the president): the Drengin are planning to attack! Build more factories! We need more warships!
Governors: No. That's scare tactics. You didn't listen to us when we wanted 1000 credits for our pork barrel projects. Now that you ask for help, we're going to ignore you. We'd rather build marketplaces because it benefits our local economy more. Your proposals are just a ploy to increase the military-industrial complex at the expense of everyone else. hahahahaha)
On the other hand, if you set up a Command Economy you'll be like North Korea: lots of control but very little resources to control.
Different civs will have different preferences. The Iridium governors if allowed to run free will spam marketplaces on more than half their worlds. Drengin governors though will just spam slave pens and factories.
You can switch between free market and command economies but this would lead to massive anarchy for several turns UNLESS one of your planets have recently been invaded or attacked, in which case the anarchy is minimal or zero.
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With this scenario different civilizations will have different flavors. The Iridium for example would have the highest economic bonuses from free market systems, BUT getting their planetary governors to listen to you is almost impossible. The Drengin, though, have no trouble at all with controlling planetary governors. Unfortunately, due to the economic inefficiency of slavery, their economy operates like North Korea or Venezuela.
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This would also help with late-game issues (where the game gets tedious) because once you've conquered a lot of planets and reached a dominating position, your planetary governors start doing whatever the hell they feel like.
