The following feedback is based on 3 playthroughs: Regular, Hard and Extreme respectively.
My perspective is that of a longtime gamer, and veteran software dev (but not a game dev). I am definitely the target audience for this type of game, and like many others on this forum, I see a rough diamond.
I have a heavy bias towards developing strong foundations for software first (in case of games, it would be the game engine), and only building on top of that, once confident that it will serve well, with no need for large adjustments. In other words, while I recognize that developing SW (including games) is an iterative process, I value design heavily over trial and error.
When I play Shadow Empire, and read the manual, it is abundantly clear that it is a work of love, and that a great deal of thought and time has gone into both design and implementation. That is why I have agonized for a week over how to offer constructive criticism.
It is difficult to offer feedback for this game, without producing a wall of text. In an effort not to do that, I will not comment on specific details of the game that could be improved, but instead consider it as being in an early stage of development, despite the fact that it is stable, fairly complete, and at least somewhat enjoyable, if you are one of the few who stick with it, and learn the game mechanics.
I think Shadow Empire's strenghts are (or will be) replayability, and the ability to expand content, like more diverse and interesting factions (particularly aliens and exotic native species). It has superb elements of storytelling from its randomness, and empire building.
The weaknesses are that its core mechanics are unnecessarily complicated, and too often subtract, rather than add, and the complexity makes the core of the game much less suited for adding content, and thus from reaching the game's full potential.
My overall feedback is that Shadow Empire should shore up its weaknesses, and only then double down on its strengths. Or in other words: There is a great game engine somehwere here, if we ask, what are we trying to achieve?
For example: Tactical/strategic games like this, often have a supply system. Why? Because we want supply lines to be part of tactical maneuvering, and maybe even the overall strategy. In Shadow Empire, we also want it to give a sense of a growing Empire.
So does the current implementation do this? Yes, but unfortunately it also makes any sane person put down the game, walk away, and never look back. The traffic lights will not save the overcomplicated supply system. Many others have already commented on the supply system, so I will not spend more time on it here, other than to say that it is very much part of the core/engine of the game, and it must be simplified.
After the supply system, the 2nd most problematic issue are the SHQs. They introduce a multitude of problems, and seem to add absolutely nothing to the game. When reading the manual, it became clear to me that they are presented as absolutely crucial, and something that the dev has spent a lot of time thinking about as central pieces of a complicated web. When playing the game, I can't help thinking about how deeply integrated they are in so many aspects of the game, that they saturate the code base, including large parts of what can reasonably be considered the game engine. It is difficult for me to imagine removing SHQs entirely at this stage, much less that the dev would want to, and yet, it seems to me, that both from a player or dev perspective, and from the games storytelling, or any other angle I can think of, they contribute absolutely nothing, while being the source of many of the game's issues. Too many to even begin to enumerate them.
In many ways, SHQs are barriers for new players, who will struggle to understand them, as we already see on this forum. The way they manage items makes it practically impossible to determine if you have enough ressources to do what you are contemplating, or if you will suddenly have you empire reduced to a non-functioning heap of bricks, because of a shortage of some critical ressource. Reloading your game gets old fast.
There are many other issues, but the supply systems and SHQs are the most significant and fundamental.
Like others, I have concerns that this game may not reach its full potential. I think that Shadow Empire is what it could be, as Hearts of Iron I is to Hearts of Iron IV + expansion + patches. That is, unless the game simplifies and shears off the complexity that detracts more than it adds, then it will be 3 remakes, an expansion and 10 years of dev time away from reaching its potential.
It is my sincere hope that we can skip a few remakes and reduce the dev time by a considerable factor, if we step back and ask the hard questions now, rather than through a 10 year iterative trial and error process.
..and so it inevitably became a wall of text anyway.