I think to achieve what you ask (ie, true differences between designs) we would need to be able to actually design the rooms themselves, not just their placement and rotation. As well as have more "micro" design ability, IE wall thickness and corridors with armor of various types, so that designs get a larger range of cost sources and saving possibilites. As it stands (particularly with the fuel tanks, engineering and cargo, we are nearly required to design ships a certain way with only marginal differences because we can not actually affect the shape of rooms ourselves.
In order to design rooms we would essentially be designing the room as a template first (like in Hospital Tycoon, placement of devices, large and small, as well as vertical access shafts, energy relays, fire extinguishers and stuff like that...) , then the room placement and rotation, and depending on where we put doors in the template the room has connections to corridors.
And as for Corridors.. I think it'd be neat if we could put (less efficient) energy relays or oxygen/water tanks into the walls of corridors (that large gap essentially that currently exists in between rooms.
Not sure that is within the scope of the this project, but I think currently the design element is too "zoomed out" ie, we don't have enough complexity and freedom to allow for truly dynamic designs.
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