I hate that mechanic, forced me to defend everything on my homeworld, because it was the only place with decent salvage percentage. Also meant attacking was risky because it meant lost salvage, actually discouraging me from taking the fight in enemy space and finding a lot of cheese to attract things on my territory.
What's needed is shorter rebuild time and more "fluid" gaming, as chemical art said.
One possible idea would be to consider fabricators "motherships" instead of fabricators, that produces "drone ships" instead of ships.
Example: you set a fabricator to build a wave of fighter, and if fighters are destroyed, the fabricator keeps track of it and rebuilts it 60 seconds later (by default, less for neinzuls, more for spire), for free. Fabricator would take a fixed metal income, and cost a large amount of metal. Same for turrets. Auto-build linked to the home station, rebuild essentially free. Or maybe a "turret station" with the same purpose, but pertaining to turrets.
So basically it would change the focus of the game toward not losing the fabricators, would allow counter attacks much faster, BUT... losing fabricators / home stations would hurt. A lot. This would also give the AI other objectives than just clearing the home station.
Another idea could be to have the ships be exponentially more expensive depending on the quantity you're currently controlling.
Yet another idea could be to simply increase upkeep costs to "more significant" level, like half of the build cost. Which would lead to higher metal gains during construction, leading in about the same effect overall.