Civilian Lines are a great start to try and combat micro-management but it doesn't go far enough imo. They are very unreliable and inexact, and can only ship facilities. What I propose instead is a sort of player-run Shipping Line that uses freighters you build and assign to it in order to automatically ship the right stuff to the right place.
The Shipping Network would handle minerals, colonists, fuel, munitions and MSP in addition to facilities. Planets can be designated as Sources for all these goods and Stockpile Quotas can be set to make sure a planet never runs low on a particular good without getting resupplied. For instance, if a colony doesn't have a source of Duranium in the system you can set a Stockpile Quota and the Shipping Network will automatically send freighters full of Duranium from designated sources until the stockpile is full enough. Planets can also be prioritized to receive shipping.
You can set Conditional Orders for the whole Shipping Network. By default, ships will refuel in-between missions and when at 25% capacity. They won't accept missions outside of their range.
The Shipping Network also applies to Mining and Fuel Harvesters. When assigned, these ships will automatically fly to a valid source, harvest until full, and then unload at the closest available colony prioritizing those with a demand for their goods and then those who source their goods. Ships themselves can be designated as sources and be given Stockpile Quotas.
Colonization can be automated as well; the player can set a 'target population' that will automatically place orders for colonists AND the infrastructure to support them. The Shipping Network will never ship colonists to a planet that can't support them.
Production Quotas are like Stockpile Quotas, but instead of relying on the Shipping Network the colony will fulfil it by actually producing the designated good. Production Quotas when set higher than Stockpile Quotas produce a surplus that can be distributed via your Shipping Network throughout your empire. For example, a colony can set its Production Quota to make sure it is always working towards having 10,000 ASMs but have a Stockpile Quota of only 1,000 ASMs, meaning it has 9,000 ASM available to export to colonies that request it. This allows you to make sure you always producing enough of a good without wastefully draining your resources on continuous production.
Ships in the Network can either be assigned to service the whole empire of a few choice systems. They can be organized into Task Groups and you can specify what kinds of jobs they can take. By default, ships in the Network will take any job they can given their design.
Such a mechanic is large, complex, and would radically alter the game for the better imo. Every game I've quit was due to the logistics spiraling out of control with no way to suitably automate them, so lessening that burden I think should be a top priority.
