There was something you said earlier in the ball-park range of it seeming like some of us just want more colony size because its more pluses, and that's not entirely wrong. In fact, it's probably, at least three fourths correct. But you have to understand something Alex. I hate to break it to you, but just about every person that plays Startsector is, to some extent, a munchkin that will number crunch the game until they can glass the entire sector with the exhaust fumes of their fleet full of cheese. I don't know how you've not noticed this in the decade-ish time that you've been working on the game, but it's the truth.
I'm not saying you have to, or even should give in to the munchkin hive-mind, but you should be aware it exists at least.
Now onto my thoughts.
Personally, I feel like capping colony size is just a solution looking for a problem. Essentially, the only problems of large Colony sizes that I can see, are the lore conflict, the lack of "realism", and the thematic issues, all things you've previously said should move out of the way for game mechanics. Those three things could be more easily 'fixed' just by reducing the population number of each colony size, or giving certain core worlds specific conditions that, for lore-reasons just state they have larger populations than what their size would otherwise state.
On the other hand, limiting colony size loses granularity. While there aren't currently any mechanics that take advantage of having specific sizes of worlds other than industry limitations, you lose that potential by getting rid of it. Also having more stages just gives players a better sense of progression and... well people tend to like it because we're munchkins. My point being that it seems like a choice that has nothing but disadvantages while the current system is just kind of... fine.
As far as mining colonies go, you're talking about trying to fundamentally work against concepts that have been implemented in the colony system. There are four reasons to have colonies: ship/weapon production, storage, tech-mining, and money. Two of these are enhanced by having larger colonies, and the rest have nothing to do with colony size. Bigger colonies make more money and more stuff. They get more market share, export more goods, and you can stack more buffs on them.
Plus, production doesn't matter beyond the profits they make. Sure, you have to make sure your colonies have access to all the goods they need for their structures/industries to function, but that's really just an extention of the profit they make. In service to this, mining (ore, organics, and rare ore) isn't even close to the highest income products, Metals Transplutonics, and Volatiles are. The income you make form ore, and rare ore are basically trivial, to the extent that you should only ever need at most one ore and one rare ore mining world to supply the rest of your refinery empire. And even that still mandates that your mining colonies have large populations for the large resource supply.
Basically, you are never going to get 'high-hazard small mining colonies' organically. Unless you hamfist it in some way, it's just not happening. It just doesn't work with the mechanics. The only option I can think of is either a fundamental change to the mining system so that more population doesn't improve goods produced, a massive increase to mining profitability just for having the industry, or effectively some kind of 'mining colony' button that limits the colony growth, but gives massive bonuses to accessibility and production (and either prevents or doesn't benefit volatiles, farming, refineries, etc).
As for requiring items to bring income up to pre-nerf, or rather '0.95' levels, once again, it feels more like a solution looking for a problem. While currently colonies can quickly make money a non-issue, that's not because they're unbalanced but because the game has a fundamental lack of resource sinks in end game. Most money is spent on maintenance through labor costs, replacement ships, supplies, and fuel, or investment through buying more ships/weapons or colony stuff. Getting a stable source of passive income fundamentally changes this, and it will always be either too much or not enough as long as there isn't something else to sink it in. Basically all you're doing is stretching out the mid game and kicking the problem down the line. It's not going to change the fact that, eventually, I'm going to have a bunch of colonies, covered in alpha cores, each planet a fortress unto itself, spitting money at me faster than I can spend it. It's the munchkin way.
I can't tell you what end game should be, as I don't know what your plans are, but I can tell your right now that farming [REDACTED] for AI cores, raiding, and colony shenanigans ain't it. That stuff all feels like gearing up for the final boss, like the Loyalty missions in Mass Effect, or getting the Master Sword. It feels like a rollercoaster about to come to a hilltop and instead of going over and finishing the coaster, you're just trying to make the hill bigger.
I'm not trying to demand 'more content', I'm saying that the current game crescendos in a way that suggests there is something unfinished waiting at the end, and that it seems to me the problem is not that the mechanics haven't been tweaked 'just right', but rather that it either needs to be changed in a fundamental way or an ending given.
Oh, and though I appreciate rolling the story points and streamlining the skill system, I disagree with the design choice to limit the number of skills a player can have (even though that isn't a new addition). Mainly because it doesn't accomplish your goal, i.e. adding a meaningful choice. A fundament problem with the system is that there will always be a 'best' skill out of every choice. You can get those skills infinitely close, but you can never truly make them equal. Because of this, there will always be a 'best' build, and players will always gravitate towards it.
To give an example, let's take that navigation skill example. The one that increases overall speed is better. Why? Because it's an overall speed boost, vs making up for a penalty. I can just limit the times when I need to 'slow-move', which I will be used to anyway beforehand. In contrast, the slow-move buff only helps in situations that are sub-optimal to begin with, and no matter how fast you go when slow-moving, I assume it's never going to overtake someone going normal speed. The choice is between lessening a penalty that happens when you essentially screw up positioning in the map, or buffing everything else. It's especially egregious because neither really defines your gameplay, it's not a meaningful choice, it's a nobrainer.
If you really, absolutely, want to provoke different builds, in my opinion, the only real option is to make it so either each choice has nothing to do with each other, or fundamentally changes the way you play the game. An example (But not a good one) would be something like Transverse Jump or Emergency Escape Jump (that gives you a way to escape battles), or 20% extra OP vs extra administrators. Again those are not suggestions, just examples of choices that I feel would be truly 'meaningful'.
What's more, it's more than likely, that the industry/general/utility skills will be, once again prioritized over the combat skills because as always, generally speaking, it's not the player's combat performance that matters most. That's... one more thing that's sort of fundamental to the game as well.
My logic is that making it either a choice that defines the way you play, or some kind of Apples to Oranges thing obfuscates the 'best option'. Despite that, it still doesn't eliminate the problem of there being a 'best choice'. And quite a few players will feel compelled to take the 'better' choice, even when they would prefer something else. Again, cause we're all kind of munchkins.
As a word of caution, any game like this that constantly drains at your resources tends to provoke min-maxing. I hate to say it, but your idea of balance tends to drag the game out and make things more difficult than they absolutely have to be. It's not a bad thing in of itself, but it does naturally discourage the organic feel you seem to be chasing. The less wiggle room people have, the more they tend to gravitate to things that they 'know' work, and the less they are inclined to actually explore mechanics. This leads into the base-bounty nerf. It's just going to further squeeze margins tighter for people. As a source of stable income decreases, the number of risks you are willing to take decrease. The less you want to buy that ship you haven't used, or try out a new fleet composition, because if you do lose something you can't afford to replace it, or the time spent to do so will set you back too far.
In other words, it means it attracts munchkins and breeds munchkin tendancies into the non-munchkins that stay.
Regardless, I hope my comments don't come off as... pushy or demanding. I believe that I don't necessarily disagree with what you're trying to accomplish. It's just that I think the way you're going about it won't get the results you want. While I certainly have my own desires for what I would 'like' from the game and perhaps I'm projecting my own desires onto you, I'm trying to go on what you've said in the past.
In the end, I'm an opinionated person, and as I write things like this, I tend to get defensive as I pick holes in my own comments. Also its been a few days since I've checked the patch notes or followed the conversation, so maybe some of these have been addressed, or are misunderstandings. I apologize in advance if this is the case.
Have a nice day.