Addressing a few of your examples:
To me, engineers is needlessly complex. Were I designing the game, I'd have simply introduced "sub-modules" that can be attached to existing modules that modify their stats with positive and negative effects. Some modules can have more than one sub-module, however each sub-module impacts the performance of the other, somes in a good way, sometimes in a bad way. It would also remove the needless introduction of RNG ( which pretty much nobody really likes anyway ).
It's complex but it's more enjoyable because you can now fine tune your ship without RNG and without wasting time running around the galaxy looking for rare minerals.
Mining is complex in a way I don't enjoy.
Humans are lazy. If we can think of a better way to do things, we will do it.
Foot > Horse > Carriage > Train > Car > Plane.
Hand > Pickaxe > Automated mining equipment.
Here's a modern prototype of an asteroid miner. Modern. As in, recently.
So why introduce a system as needlessly complex as velcroing a laser to the front of your ship and then manually scooping minerals as they separate from the asteroid, or sacrifice cargo space with limpets and then still have to refine the material? Why can't a miner simply sell the raw stuff, why does he have to fashion gold bars? Needless complexity.
What's wrong with a mining drone ( see above ) that extracts the minerals, dumps them into a cargo container which you then have to collect from the asteroid with your limpets?
And it can get more fun if you can have multiple mining drones at once. Complex, but uncomplicated and easier to manage.
Trading, IMHO, needs a massive overhaul.
To begin with, I should not have to go outside of the game to find better trading routes because trying to find them in-game is needlessly tedious, needlessly complex, needlessly needless.
There is no reason, at all, why humans can travel through space at FTL speeds but not have discovered a way to communicate with each other in a more effective manner. We're already studying ways of creating FTL communication systems. It makes absolutely no sense for humanity to spread across the stars and NOT have an effective communication system in place first. That literally goes against who we are. Would we have sent people to the moon if our only form of communication was morse-code on a flashlight? No.
Instead, we have an economy that denies logical explanation. Hundreds of star systems in the bubble, and the economy is run by traders because there is "no other way" to communicate with allied or competitor stations? Really?
Of course, this inability to communicate is further compounded by the fact that some random mission giver can send you a text message 200ly from away, but stations next door to each other can't.
Needless complexity results in disjointed elements of a game.
Complexity can be a good thing but in moderation and not just implemented "because we felt like making it complex for the sake of teh gameplay."
If there's a valid reason for the complexity, it's implemented well
and keeps you entertained as you do it.. I'm all for it. Otherwise it's just .. a pain.