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Due to the game mechanics, the most efficient ship design is a really big square. This could be changed by having more modules use exterior space the way the hyperspace drive and airlock do. Making the perimeter of the ship as much of a resource as the area would lead to more interesting decisions about how to build. This might even make having multiple ships worth the trouble. Things like shields, hull integrity, solar panels, shuttles, and mining pods would be good candidates for external modules. Admittedly this would be a lot of work, but I think the boring ship designs really need to be dealt with.
That's an interesting idea, although it would require proper scrutiny to find out if it really works. =) Depending on how the exterior requirements are set for different facilities it could render some ship designs completely useless, as there would simply be no good places to put certain modules.

What I'm talking about now is ship designs in terms of "looks". It is true though that there are optimal ways to construct a ship, to make path distances shortest possible etc. Is that a cube? Seems so.

Right now the square is just a canvas, like a canvas to paint on. It's not meant to be a design in itself, it is meant to function as a canvas and give the player the maximum freedom to design a ship, sandbox style. If the canvas itself was in some ship form from the get go it would actually be more limiting, it would force the player to build a ship like that.

We haven't dived deeper into this yet, but it has been on our minds for a longer time. We'll see how it evolves in the future!