Possible proposal 1: remove penalties from all force fields.
Honestly, I don't see where this would be such a bad thing. Fortresses and other uber-powered defenses could possibly stay hampered by forcefields, but what would the other implications on balance be? Are turrets really that powerful (which I know the subject is being discussed elsewhere), especially considering the AI's default options for negating forcefields (Raid and Plasma Siege for subversion, Bomber and Spire for direct assault)? Obviously this would require a buff to lightning and flak, but I don't tend to put them under forcefields anyways --- perhaps I'm doing it wrong, but I tend to have more important things to protect, especially since I play with Exos on.
Possible proposal 2: as long as fabricators/factories are captured, their build options are added to basic stardocks/starship constructors.
This reduces to one of the potential new hacking mechanics that Keith mentioned before, which seems the best way to handle this (given the differences of opinion on destructible capturables and the like).
Possible proposal 3: remove golem self attrition, make them weaker if needed to compensate.
This is what prompted me to reply, because I was just thinking about that (again). If the purpose of the attrition is to require a constant resource cost for "maintenance," then why not just place a direct resource cost on Golems? The attrition doesn't seem to be steep enough to be have a significant strategic impact --- yes, it does have one, but you can usually take your Golems about as far as you'd want to go without having to worry about not making it back through the systems you decimated, at least in my experience.
The current mechanic strikes me as a lesser version of the "making change for a dollar" system that prompted the energy remake.
Possible proposal 4: instead of exos for golems, add 1 golem to every wave for each golem that was activated during the game.
I don't think that getting rid of Exos entirely is the solution, and adding Golems to waves will only end in pain.
I remember when I brought up only starting the exos after capturing Golems, one of the counters was that it encourages waiting till the endgame, capturing "ALL THE GOLEMS!" and proceeding to curbstomp the AI before it could respond. However, maybe it would be possible to do something like the Champion Nemeses, where the homeworlds receive a Golem when one is captured. You could heavily play with the system, including things like respawn frequency, behaviors, etc. to make it balanced without the treadmill effect. All in all, the superweapons appear due for a rebalance due to the SS buffs (though shifting the core ships down is certainly another way of doing it); it may be worth considering non-numeric balancing options as well, instead of continuing on the treadmill of constantly increasing numbers.
Possible proposal 5: make shield bearers always available to players, maybe also always available to AI, hopefully they can be better balanced, or at least everyone gets to share in the huge fun of having them.
I'll leave this one to people with more experience in ship-vs-ship balance. Personally, I think that shield bearers seem to be fine as non-automatic ships, and there's plenty of other ships that the "fun times all around" argument would apply to.
Though I still think that fixing the 16-ship-limit in the UI and having an option for "all ships unlocked" would definitely be fun. (I've still never figured out how Cinth games the system to work around the UI, other than queuing up the ships before they disappear.)