I don't have any issues with any command stations at the moment. I haven't tried the new mini-forts out yet though (although I think they should be altered before military stations since they're new and people have generally been happy with command station balancing till now).
I personally use logistics, with military command stations on whipping boys or satellite worlds (unless the translocation has a negative affect, eg fabricators in remote locations on the planet).
Logistics stations should not be underestimated tbh, I recently played a 120 planet 1HW take everything FS game resulting in over 2500+ AIP and the highways I made from my FS cities/fabricators and major fleet building worlds were essential.
Any planet that didn't have ships traveling through often had economic stations. So I think they all serve their relative purpose well. If we were to add additional features to command stations I think these should be further knowledge unlocks rather than being bundled with the current.
EDIT: Was just reading a suggestion about logistics IIIs being able to 'warp' you to other planets - this to me seems very OP. However I like the idea and offer a counter but kind of off-topic suggestion- Since we have research and knowledge hacking why not add warp gate hacking. You enter a hostile planet, a special ship, lets call it the warp network interceptor allows you to select a *scouted* planet that has an active warp gate, you then spend x minutes hacking the warp gate and once its finished you can send a fleet through to the destination you chose. How the AI reacts (whether it reacts whilst hacking or on the otherside of the warp (or both) can be decided if anyone thinks this is a good extension of the idea
)