Personally, I'd be happy with Military Starbases if they just
scaled better in survivability. Even at high techlevels they DO provide useful benefits, mostly for smaller hull sizes but every bit helps - they are just way too flimsy.
A couple of fairly simple ideas that hopefully aren't too unbalancing:
* Add another 2 Fortification techs (IV and V) with even higher level attack/defense modules. Starbases are supposed to be huge and probably have way better energy-generating abilities than you can place on ships. As such, it would be nice if they had real teeth also in the end-game tech race. When the choice is between investing 5-8 constructors or 30+, the latter supposedly to make the starbase armed and dangerous, it would be nice if it was actually armed and dangerous requiring significant resources to take down.
* Increase starbase hitpoints across the board with each starbase fortification tech. Say another 50% of base hitpoints per tech for non-military starbases and 100% of base hitpoints per tech for military starbases.
* Increase starbase attack/defense by miniaturization... Hey, if the components are smaller on the ships so there are room for more of them, that's probably the case on starbases as well. No redesign of starbases needed, just increase the attack/defense values as if the extra space in each component was utilized properly.
* Better self repair...
More far out ideas...
* Let ANY combat action that occurs within range of a military starbase suffer one (1) initial attack from the starbase at a strength that depends on the distance from the starbase (50% of the starbase range from the starbase gives a 50% attack) before fighting between the participants take place (yes, that includes multiple starbases firing their one shot or even starbases firing in support of other starbases).
* Let a military starbase cause losses to any troop transport attemting to invade a planet within its range. If you need an explanation for how it can do this, just assume that a military starbase has a contingent of small fightercraft that you never see on the map (they are even smaller than tiny ones, some that cannot travel far on their own)... If really pedantic, slave that ability to having upgraded with the fighter-drones.