I feel like it's easier to find places to put Military command stations than to put Economic or Logistics stations. I'm going to have whipping boys, and those want Milspec. I'll either have chokepoints and outposts in front of the chokes, in which case those all get Milspec, or I don't have chokes and most of my planets are going to get Milspec stations because they're not isolated from the front lines. Even then, I think Milspecs are good enough to be worth it even if you don't use all 12 stations, because a single Mil3 can make a huge difference if it's in the right place.
I only feel comfortable putting economic stations on protected, non-front line planets. I've never had a game where I owned 12 planets that met that description (granted, I'm a noob, but it still seems unlikely to happen much with my low-AIP playstyle). And if I don't place all 12, I'm not getting full benefit from my K.
The extra energy production makes these a lot more attractive, because if you're trying to keep AIP as low as possible, and you like core turrets as much as I do, energy is frequently pretty tight. That exacerbates the problem of having planets to put them on.
Same for logistics planets: those go on high-traffic planets that I'm moving fleets through a lot. I've never had 12 of those at once. Even when I have a high-traffic route, I don't necessarily have all the planets in it, so having logistics stations spread their benefits to adjacent planets would make them way more attractive. Even just spreading the speed boost would be nice, and I don't think it would affect chokes much. Hell, make LogIIIs project their speed boost two planets out. Or grant supply two planets out, so I can build even deeper core turret beachheads. =P This might be map-dependent, also; snake/vine/tree maps probably get more benefit from these.
There's also the matter of the tradeoffs involved. Economic command centers compete with just capturing more planets, waiting longer, and especially upgrading metal harvesters. If you have enough planets to place 12 econ stations in reasonably safe locations, you have enough planets that you probably could have just gotten better harvesters. The energy change makes a big difference here, though, if you can use it. Golems-Medium comes to mind.
Logistics stations compete with... transports, I guess? Waiting longer for stuff to get places? And those wacky Zenith SpaceTime manipulators, and gravity turrets. And slightly with economic stuff due to their higher salvage percent. I feel like that's some very stiff competition. Also, at least some of their awesome seems aimed at putting them on chokes, but if the command station goes down, so do all of your defenses, and Log stations are squishy. And Military command stations are just generally better.
Buffing the hp of econ/log stations would make me feel better about putting them on front-line planets, which would make it easier to place them all.
Lowering their caps and knowledge cost would also make them easier to fully leverage, especially for the MkII stations. That way if you have a couple of planets that seem like really good places for Econ or Logistics stations, it's a much smaller investment to be able to put down a couple of good ones. Cap of 3 feels right to me, I can find 3 econ-worthy planets if I need more energy and metal. Then once you hit 6 planets that want econs or logs, you can get MkIII and upgrade all those planets to MkIII, and then re-use the MkIIs as you get up to 9 planets of that type.
Military command stations feel like they should be the opposite, with the MkII keeping a cap of six but the MkIII going down to a cap of 3 or 4, possibly with a reduction in K cost. That way you can support your chokes and a few outposts with MkIIs, or have really strong chokes and more outposts.
Obviously, that's a pretty big change, and I think the current philosophy is focused around making the MkIII stations really awesome to justify the high K investment. I think this would make the MkIII econ/log station unlocks more valuable, because now they're better and have a higher cap and the total cost is lower.