Add beneath the capital ship and logistics upgrades of all races a new upgrade tree. This would deal with fleet logistics efficiency for individual units. What i mean by this is, it would give your fleet more capabilities by fundamentally altering your fleet logistics to cost ratio. There should be a permanent drawbacks, much like once you have teched up logistics, you can't unresearch that investment to get a reduced income penalty.
Say you want to make your LRM's cheaper logistics wise. You would research the tech (probably tech level 5-6) and gain LRMS that were cheaper on logistics use but with a reduced capability, lets say speed. This allows you to field more earlier, but at the same time you have permanently reduced your fleet capability in one aspect.
This allows people to have slightly tweaked fleets that will only add to the games replay value.
I wonder how many developers will cringe at this idea? lol.