Orbital stations are in a bit of a strange place currently:
Military stations are fairly effective against early Marauder and Harpy incursions as well as against AI attacks but cost a ton of metal thus player can find more effective defense and AI is slowed down by these as they are producing tons of such stations instead of ships.
Now for the AI, producing more then two military stations is less then effective as:
1. One is enough to repel Harpies and Marauders as mentioned above, and two are overkill (waste of their resources).
2. The AI will still produce two military stations for each of their front line planets to "defend" them but this is neither cost effective nor enough to stop a Human lead invasion force as concentration on Railgun pretty much counters the stations
Thus I suggest that all military stations are limited to a single instance per planet and if we are already on it, have the rule be valid for all types of stations which are:
1. Space stations / Mobile Base / Asteroid Base (Commercial)
2. Shipyard (Commercial)
3. Starbase (Military)
4. Fortress (Military)
As visible above, there would be still a ton of personalization options with the above, especially if Stargates would also occupy one of the two available slots to make the decision building them more meaningful: 14
! to be precise (+ the flexibility of adding Construction modules or Research stations to military bases and Bomber squadron to commercial ones)
1. Prevent "Fortress worlds" with two Fortresses: waste of resources and boring for the player to mop up (There is nothing wrong with the AI building bases but should invest in fleets as well). More resources left for the AI = more ships defending their systems
2. Also forces the AI to build more sensibly as no duplicates allowed
3. A bunch of the above options cannot be duplicated already: for Shipyard does not make sense, for Stargates not an option
4. Prevent also the player to turtle in too heavily
A further bonus of limiting all base types to just one per planet is the increased weight for each build:
1. If faction specific stations would be introduced, they can be done on the first military level: for the Starbase, and limiting their number to just one per planet would prevent obvious exploits as well as balancing issues if the Starbase of one race is less capable in defense and geared more towards commerce (Phidi). As there can only be one aesthetic value increased of the new art as well as any relative disadvantages as well as faction specific advantages provided by the layout can be kept in check.
2. Forces a more dynamic build approach for the first tier military base, as there cannot be any other further military base until Fortress is researched
Incidental I would also advise assigning a hefty upkeep cost for Fortresses to further emphasize their circumstantial role and deter Fortress spamming all over the galaxy, even if reduced to a single base per planet