I still like the idea of having modular command stations. Can it be done in such a fashion that you can place upgrades on a command station that unlocks certain builds? E.g.
You start out by building a regular command. Then you can choose a specialty (Military, Economic, or Logistic). This specialization unlocks a small system cap of items that you could build there, such as turrets, higher mark resource gatherers, or ship building and speed enhancements. Then with the right research, you can upgrade some of them to the next mark higher, increasing the system cap of whatever their specialty is (and possibly adding a small cap of turrets to the mix), and once again a few more to one mark higher.
For example you could have military command stations unlock like this per rank:
Mk1: Railguns, limited tachyon, 5 turrets of each basic type, 1 shield of each type (Individual turrets still need unlocking and HBCs non-withstanding)
Mk2: Engine destroying Railguns, extended tachyon, 10 basic turrets and 1 shield of each type
Mk3: Paralyzing railguns, system tachyon, 20 basic turrets and 2 shields of each type, 1 non-modular non-super fortress of each type available (if researched)
Economic:
Mk1: 40 resource income + 20 per harvester at Mk3 (via research)
Mk2: 40 resource income + 40 per harvester at Mk3, resource nodes in system are upgraded to Mk2 for free (research upgrades can override this to Mk3)
Mk3: 40 resource income + 60 per harvester at Mk3, resource nodes Mk3 + Harvester Exo-shields and 5 basic turrets + 1 shield (Minor protective measures of a key resource system)
Logistic: (I personally don't use logistics stations. I don't really see the point. I'll add something of my own idea here.)
Mk1: 20% speed boost in system. Engineers in system get 10% to construction/repair speed.
Mk2: 50% speed boost in system, lasts for 10 seconds after leaving. Engineers get 25% to construction/repair speed. 5% construction cost reduction.
Mk3: 100% speed boost in system, lasts for 20 seconds after leaving. Engineers get 50% to construction/repair speed. 10% construction cost reduction. Enemy speed inhibited in system. 5 basic turrets + 1 shield (Minor protective measures for a key production system.)
Of course the knowledge cost of unlocking the upgraded stations would probably go up a bit, but I think this would make the game less: Oh this system is way out of the way, the AI will never attack here. 0 resources? Mk5 factory? Who cares, derp Economic Mk3. Instead it'd be more: Crap, there's a lot of resources in this system. It's not on my frontlines, but it could see some action. Let's put a Mk3 here and get some minor defenses to hold them off while I get my forces to help. Over here with 0 resources and a Mk5 factory, lets make this a logistics system to help produce ships for my war effort.
For the record, I don't use Logistics bases at all really right now. I just produce ships where I need them, so what's the use?
Final edit: Home command station should possibly have some of the benefits of the military and economic stations as it is unique, but that's up for discussion about quite how much it should get.
Ok I lied, real final edit: Anything I say specifically the station allows, gives it to you without the K unlock. This includes harvesters, and Harvester Exo-Shields. However this is only for that one system. Other systems do not get this bonus. It is up to the player at this point if they wish to unlock that research for broad usage. Think of it as the Economic Station comes with the knowledge of how to build versions of these that only it has the capability and resources allocated to support it. The K unlock version is a more efficient version that any station can support.
Turrets however do not get auto unlocked. To clarify though, what I mean by basic turrets however are: Basic, Laser, MLRS, Missile, Sniper/Spider, Lightning, Flak, and Tractor. Turrets like the HBC, or Gravity, or counter X still have a Universal cap, as they are more specialized, and not as needed in clusters. With the proper K expenditure, you can have up to 60 of each (40 for sniper types) in up to 6 Mk3 systems, but this also requires spending the K to unlock the Mk3 combat command station.