Modules that process ore into refined materials. Ore prices could go down because people wont have to fly too far to sell it, and refined commodities prices would go up.
A factory module that makes special ships, (like a 8k cargo super transport).
Electronic countermeasures defense modules, driving torpedoes away from the base, or disrupting enemy ships electronics when they come too close, reducing the radar detection range, etc.
Long range scannner modules, issues a system warning when a specific tagged ship shows up in the system.
NPC docking bay, stores a bunch of fighters/bombers that auto deploy when the base is attacked.
Resupply module, produces nanobots/regens.
Research module, produce nomad flashy thingies from nomad remains.
Evil module, produces evil drones from children tears for all your <strike>corporate</strike> evil plans.
More variety in modules would give bases more roles, resupply + npc carrier module could be combined to create a military outpost of some sort. While research module+ECM module would make a good combination for a supar sikrit research base, currently player owned bases are pretty much the same.
Some ideas here are not really feasible, or would require enormous ammounts of time to balance, I just made them up.