Had a thought regarding starbases and keeping them alive later into the game. Apologies if this has come up before but...
...make them shoot more than once per round.
As you upgrade them, let the modules add to the shot count. For example Battle Stations I shoots once, Battle Stations II adds another shot per round, Battle Stations III adds another shot per round... or two or whatever balance requires.
Or whatever module you want to attach it to.