Many of the things later on in your list can be easily modded.
Try the leaky armor system.
Try requiring armor mounts which base protection per kt on the total hull size.
Fiddle the mounts and racial costs as you suggested.
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If this is not already true, and I think that it is not, I would like to see damage randomization weighted by the larger of structure space and the damage size of a component. The chances of hitting a Large Weapon should be greater than the chances of hitting a 10 KT component.
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A 50-hitpoint component is at least Five times more likely to be hit than a 10-hitpoint component.
I believe it is slightly more than that, but there is room for doubt.
Armor works the opposite way, with weaker components being destroyed first.
Just mod it!
Then start a PBW game and see how many people agree with your changes 