Outside of an expansion or mod, I can't see anything really progressing here. There really just needs to be more advanced defences. Expensive so they couldn't be massed, but powerful enough to give even HCs a fight. Starbases and heavy defence platforms.
For what we actually have to work with, I would really just like to see defences scale better throughout the game. A turret works fine on a basic frigate, but once LRMS and carriers show up at tier 2/3 they're now useless forever unless you mass 20 of them. Weapon and armor upgrades should affect turrets more, maybe with a scaling cost to prevent extreme turtling. Like instead of a 5% damage bonus per research they get 10%. This would insure that you don't need 5 turrets just to have a chance to kill a lone HC.