That is exactly the problem I'm having with the whole ship design thing. The problem with the volume scale, shortest length thing, and damage having to work it's way in from outer tiles is that it's just going to turn into cube building simulator 2013. Which is probably realistic but not very fun. . .
Depends how you envision it working. The way I see it the reason we envisions ships and rockets as pointy is thanks to sea or air drag slowing cube things down.
That is not really acceptable though in space, at least not when you build ships in orbital space shipyards. Perhaps in a game where you build them on the ground and they get prohibitively expensive to launch unless they are pointy it could work.
But what can be done to promote the same behavior is to promote small frontal areas/ cross sections for other reasons.
Some possible other reasons:
* Minimize chance to hit debris/junk/asteroids
* Minimize area to be hit when going straight towards or away from an enemy (requires directional damage model).
* Building time scaling with minimal width, since a cube would take much longer time to build (layer by layer) then a long craft you can build in sections.
Or a combination of:
* Lowtech Reactor / Radiation concerns (reactor in the back, heavy lead in the middle and crew in the front). Small cross-section needed to minimize heavy lead needed.
* High tech FTL/Other propulsion Technobabble reasons.
I'm thinking instead of encouraging 3x3 modules to have patterns provide bonuses. For example having the modules in a cross shape would be the most effective. The problem is coming up with an intuitive system which isn't too complicated yet leaves room for creativity.
Perhaps something like supreme commander? I really loved how they made synergies between storage - production - usage of resources.
Basically you wanted a powerplant to be surrounded by energy storage to maximize efficiency bonus. And for example a shield array got a bonus if all sides are adjacent to power generation. So you could end up with shield in the middle - powerplants around it and energy storage in layer 3.
Not sure what resources and bonuses can be applied to a space game besides energy, but perhaps CPU, crew terminals (as you said) and coolant.
Crew basically just assumed to be where they're supposed to be, crew member dies if terminal he is manning is exposed to vacuum, no boarding, or other cool stuff. All this actually makes the "cube is best design" problem even worse though.
Remember that spaceships (designed for combat) would probably work like submarines though, so for every station you have 3 crew rotating 8 hour shifts. This is also because of redundancy even if someone dies or get sick there are at least two others that can take over the job.
Speaking of expensive launches, Something I really miss in Aurora is a good early model for the $ per ton cost to bring things into orbit. Most agrees that this is the number one thing holding our current space exploration back, and many different projects, ideas and theories exist to reduce this cost before real large scale space exploration and exploitation can start.
There could be various level of detail to model both infrastructure capacity (how many tons / month our current rocket/shuttle infrastructure and production can launch), and the cost of launches in fuel and cash.