For the planets, it feels like a classic "overdesign" problem to me. Lots of systems, and you get lots of complexity for not a lot of "fun" yield.
The current setup:
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Planets have inputs, buildings and starbases modify inputs by percentage yields, and you get outputs.
That could be fine, but we want to support multiple levels of buildings for upgrades, and we want to support adjacency bonuses.
So we need to make those percentages be pretty small. At the same time, we want to support lots of planets. (Core worlds/colonies helps with that, but colonies really only take you so far.)
So example with simple math:
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A planet has 20 input production. And you want to increase it. So you build manufacturing. In a good spot. +3% manufacturing. Now you have 20.6 manufacturing. Was that a fun gameplay loop? Eh. Numbers went up but not very much.... Low reward.
Well, okay, so you build another one. +1% from adjacency. And this time a +4% bonus to each. So total +8%. Now you're up to 21.6. Woof. So after multiple periods of decision and turns waiting you've gained 8% build power. From a literal empty board.
In something like Civ, you would place a worker on a production vein and gain a massive boost from the empty board. You would make a choice, and it would have a large effect. Early on, and that would set the tone of your play.
Personally, I'd much prefer a system more like MOO or Endless Space where you have pops (Endless Space 2's construction system is quite nice and nails the theme well). Each pop working a resource provides +N to that resource. Or if you want it building bases, make a "pop" a building. And once it's built, it can't be reallocated.
FOOD:
2 workers (+1 food each [base])
2 farms (+1 food each [base])
PRODUCTION:
10 workers (+2 production each [overlords social policy])
5 factories (+2 production each [megafactories built])
Adjacencies, don't need to be factored in. Heck, even Civ 6 is getting blasted in latest re-reviews for it's adjacency system and that's like it's whole thing. And if there's no adjacencies, then it really doesn't matter *where* the buildings are built. Why am I trying to figure out what state to build my Gigafactory in? Gimme one. In the system. Done. Now that system has gigafactories.
Of course I don't think that change is going to happen in this version. It would be a silly huge change again. And galciv has always leaned a bit more toward the simulation side of things. But I do wonder if perhaps those of us who love the crunchy systems of 4x games are getting way ahead of everyone. Trying to pack all of these systems together, shipping this thing that is bursting at the seams out, and forgetting what a simply, well-designed game looks like. But you asked, so...
This is really good feedback. It does seem like there might be an opportunity to do something like you describe here:

So we have the citizens and we have:

I get what you're saying that the improvements themselves are pretty grognardy and minor.
I think think the main issue here is that there isn't a mechanic that really feels satisfying but limited. Like, if you could make a big difference by putting a worker on a given tile or something.
I personally like the adjacency system a lot. But on the other hand, even there, the adjacency system isn't designed to turn a low performer into a mega performer because otherwise, *that* would be the whole game. Rather, the intended point is to tempt players to not simply do the same thing for every core world (which is one of the reasons I don't play Civ games, every city is basically the same).
I'm going to have to think about this.