In solo what bother me in the mid and end game is the pop shuffling, garding way points with minefields and other petty things like that. I really dont want to spend half of my turn doing such ininteresting things, I prefer to concentrate on military affairs.
Also I would like to find a solution to handle production list efficiently and rapidly. All these tons of mines, fighters and troops produced each turns by my planets are too much time consuming too.
My current implementation is to have the largest planet of a system as the imperial center, and a cargo on repeat load units produced on the other planets (of the system) and dump them into the imperial world. On this world I know that there is stuff waiting for me, and not elsewhere (for this given system).
Also I tend to only build a single shipyard for each system, on this imperial world, and a slew of shipyard base on this location. With this all the production and military is concentrated on a single world. The other planets either produce units, or do nothing.
In solo, mind you. In multi I would optimize and bean count to death
So, about you, how do you handle the huge micromanagement which appears more and more as the game grow older?