Star Control 3 is... about as well regarded by the fanbase as Masters of Orion 3, i.e. in need of an exorcism before it can be safely burned at the stake.
If you want to go back to Star Control 2, there's an updated open source-port of the 3DO version called The Ur-Quan Masters. Still a great game.
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If you haven't tried it, I recommend having a look at Dwarf Fortress. The world gets procedurally generated from the tectonics up, then centuries of recorded history would fill a a fantasy epic if someone was to flesh out the recording style. Everything is simulated, from social interaction over fluid dynamics to the engineering calculations of bronze impacting bone through a layer of mail and flesh.
Features beekeeping, metallurgy, terrors to awaken by digging too deep, artifacts, necromancers, the difficulty of keeping one's dwellings clean of blood and vomit, mechanical wind-powered computers, terrible vermin, troublesome nobles, magma-based solutions to troublesome nobles, cats taking over the world, graphic dismemberment, touching displays of familial affection, mothers taking their newborn to battle and using them as shields, recursive engravings of dwarves engraving images of dwarves engraving, insanity, elf-trolling and the need for alcohol to get through the working day.
It defaults to ASCII graphics and the interface is awkward, but it's quite an experience.
Somewhat less insane, but comparable in depth, complexity and WYSIWTF-compliance: Aurora.
There are many fine 4x games set in space that allow more open progression than pedestrian earth-bound ones... but no other I have played goes quite as far.
Again, emergent complexity at its finest... and offering ways to stay on top of it and reduce the micromanagement, from conditional orders to the ability to let the civilian sector handle many things. Unlike in many other games, logistics is of considerable importance. I don't cnsider it a chore because it ties neatly into sexier parts of the game - for example, it's possible to build ships a good deal more powerful than the norm at your tech level, at the cost of incrased breakdowns, high fuel consumption, and the tendency to spontaneously explode at an awkward moment.
The best things are free, what you pay for is convenience... as in some other fun aspects of life