One of the things that's been kind of circling around in my head is kind of hard to describe, but I'll try.
When you design a starship (or a starbase, or a lander, or a floating castle, etc), there are certain things that are required (engines, places to live, electricity, etc), but there are a also things which are optional, depending on the nature of the mission. For example, solar panels vs nuclear generators. Comm dishes vs heat shields vs planet-scanners vs docking systems...
There are a wide variety of things which may need to get done on any given mission, but fundamentally the missions tend to be very slow and limited. If I launch a mission to Duna, it has one particular purpose and is engineered to do that one thing. If I want to do multiple things (for example, land and then return home), I would typically build several vessels, each of which has one particular task. Sometimes vessels would be strapped to other vessels, sometimes they would be largely independent, but either way the design is "a lot of single-purpose vessels".
A big part of that is simply that Kerbal's focus is fuel restrictions. If you turn infinite fuel on, you can easily create a multipurpose ship... but the "multipurpose" is really just "landing and launching over and over", which isn't terrifically interesting.
I was thinking: what if we build a multipurpose ship instead?
This is a little bit of a difficult topic, because "multipurpose" is pretty vague. Kerbal has a pretty limited set of purposes you can multi, so let's invent some that Kerbal doesn't really cover. Let's say we want to build a ship that can do orbital transfers, planet-scanning, aerospace maneuvering (not just landing), sample collection, research, and launch.
Ordinarily, the way we would approach that would be to stick modules serving each of those purposes and try to make a ship that could do all that at once. So you'd have this big, knobby research module and you might start to consider maybe leaving it in orbit, etc.
Instead, what if we presume we have quite good 3D printers aboard our ship?
This means that our ship can "transform" by deconstituting our special equipment, then reconstituting a different set of special equipment. So we turn our solar sails into wings, turn our wings into treads, turn our treads into vehicle bays, turn our vehicle bays into research stations, turn our research stations into launch components (heavy rockets)...
It sounds overpowered, right? But we can add in some really fun restrictions.
1) Fab size constraints. Each mode you add takes up more space in the computer/fab labs, which are a constant through all modes and therefore add to the size of each mode... effectively making space and mass requirements more like "modes ^ 2" rather than "modes ^ 1".
2) Core structural constraints. The fab can create all sorts of complicated stuff, but it can't create strong structural components. Therefore, your ship design is as much about the underlying frame you create. The frame contains both internal spaces (heavily shielded and resistant to acceleration) and external spaces (along the surface, or along beams projecting out from the surface). It can also be fun to create an adaptable structure, such as heavy "wing guide" struts that can extend at various angles to allow for various kinds of modes to have various topologies.
3) Reused elements. Modes which share elements can be transitioned between quite quickly and easily, since those parts don't have to be changed out.
4) Direct interaction as astronauts, robotic arms, hinges, or sliding rail systems change the specific layout of a mode without actually changing modes. For example, changing the angle of wings from re-entry to cruise.
5) Speed of transition/prep space. In any given mode, you can add in "prep" spaces. After the mode transition is made, the prep spaces begin to fill with parts for the next anticipated mode, allowing you to shorten the final transition time quite a lot... but taking up a lot of space.
And 6) Available resources and means to gather more.
By allowing players to create a good fundamental layout and then design multiple modes of operation, you can allow players to build a bunch of ships in one, and switch between them depending on the situation. Of course, that means the situations have to vary so there's some reason to do that, which means it can't play like Kerbal. It has to vary much more than that.
We should also consider not just starships, but also space stations and settlements. How would mode-changing fit in with something like that?
Fundamentally, the situations a starship will tend to find itself in are different from the situations a base finds itself in. A lot of the things a ship does involve moving around - hence it being a ship. Bases, on the other hand, mostly just sit around. The situation doesn't change much, and they tend to run on automatic almost all the time. So switching modes is hard to make compelling for a base, since they rarely have any reason to do so.
Instead, let's think in terms of modules.
When your construction ship arrives in orbit around your destination, you'll need to construct a base.
Let's say that the base being constructed can be made out of modules rather than as a single unit. By stacking modules (space station) or linking them (ground station), you can create whatever base you want piece by piece.
Therefore, in our design phase, we can do the same thing that we do for a ship - create a basic module frame that can interlock with itself, then create various modes for it. Unlike a ship, the modules don't need on-board fab labs, so you can create a lot of different variants. Then you load up the construction ship with a number of those frames. Since they interlock, the empty frames hulk out in front of the construction ship, many times its size, just locked together in skeletal form until ready to be unlinked, filled in, and fitted properly into permanent place.
With this constraint (all modules in a base must have the same fundamental framework) we can make the same basic gameplay (designing modes) work both for ships and bases. Of course, the game would still need to be designed such that the actual moment-to-moment situation was complex and changing enough to make that modular design worthwhile. If you can plan ahead too easily, then you could design too easily.
Perhaps something like a "mission" mode would be worthwhile, where any given ship or base is in the midst of some kind of evolving situation that couldn't have been predicted back home. Anything from getting caught in a permanent hurricane to being infected by an alien virus to having to deal with a metal-eating radiation to discovering that a valuable deposit of unobtainium is laced with dangerous screwyouium. Or maybe even something like a crew member ascending and gaining psychic powers, and trying to come up with a layout that uses those new powers well.
A lot of functionality has to vary wildly based on the situation. Physics stuff, sure - but also things like research, data transmission, fuel harvesting, and so on. As the mission's conditions evolve, the player will need to choose whether to deal with the screwed-up parameters with additional resources, or just eat the penalties.
Anyway, that's my thoughts on the matter. I really do think that designing a core frame and then fleshing it out with "modes" could be very compelling.