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I have a few more technical questions so I can start designing the systems properly.
For planet occupation, when you say a star system has to be fully occupied before the player can unlock the next one, what exactly counts as fully occupied? Does every planet in the system need a certain number of humans, structures, or a specific amount of development? Can the player choose which planets to develop first, or does the game require a specific progression?
For humans, are they an actual resource or population that the player manages? Do humans need food, water, oxygen, shelter, or other things to survive? Can the population grow naturally, or does the player transport new people from other planets? Can humans be assigned to specific structures such as Labs and Miners? If a structure requires workers, does it stop producing resources when nobody is assigned to it?
For structures, do you want the player to freely place them anywhere on the planet, or are there specific build areas? Do structures have physical sizes and shapes that affect how many can fit on a planet? Can structures be moved after they are placed? Can structures be destroyed or replaced? When a structure is upgraded, does its appearance change as well as its functionality?
For the Airlocks and Tubes, do you want the player to manually draw connections between structures? If so, should the game prevent invalid connections? Can one Tube or Airlock connect multiple structures together, or does every connection need its own piece? Do resources automatically find their way through connected Tubes, or does the player need to manage specific routes?
For resources, can resources be stored locally on each planet, or is there also some kind of shared empire storage? If a Miner produces Iron, does the Iron automatically move through Tubes to a storage structure? Can resources be transferred between planets only by ships and rockets? Can ships carry multiple types of resources and humans at the same time?
For ships and Launch Pads, what determines how much a ship can carry? Do different ships have different capacities and speeds? Can the player build additional Launch Pads to increase the number of ships operating from a planet? When two planets have ships traveling between them, do you want a visible route on the galaxy map? What happens if there are no available Launch Pads or ships for a requested trip? Does the player get a notification, or does the shipment simply wait?
For Probes and exploration, when a player sends a Probe to a newly discovered system, what information does the Probe reveal? Does it reveal the planets, available resources, environmental conditions, and other useful information? Is there any reason to send multiple Probes to the same system, or is one Probe enough?
For the galaxy itself, how large are you imagining the full galaxy to be? Are we talking dozens of star systems, hundreds, thousands, or something much larger? Since the player eventually needs to reach every system, I need to know roughly how much content the game is expected to handle.
For progression, when you say planets become harsher as the player progresses, what does that actually mean mechanically? Are there environmental hazards, higher resource costs, stronger requirements for keeping humans alive, or something else? Do harsher planets provide better resources to compensate for the increased difficulty?
For the end goal, once the player reaches the central black hole, what does building the sphere actually involve? Is it going to be a massive construction project requiring resources from across the galaxy, or is it more of a final structure that becomes available after reaching a certain progression point? Once it is completed, does the game end, or can the player continue expanding afterward?
For the UI, do you imagine the game being mostly mouse driven with menus and buttons, or do you want keyboard shortcuts and other controls as well? For the planet screen, do you imagine the player looking at a side view of the planet with structures placed on the surface, a top down view, or something more like a 2D space station building interface?
And for saving, I can handle the save system itself, but we can decide the exact storage location once we know the target platform. I can also build the settings system with the General, Graphics, Audio, and Accessibility sections you mentioned so those are structured from the beginning instead of being added later.
Once I have these answers, I should have enough information to start turning the game design into actual systems and figure out what needs to be built first.