I double or tripled armor and shield slots. the nice part of doing this is that it is still balanced with cost. you can make a super dupper unkillable deathstar. but you are gonna pay for every inch of it.

when it is all resolved i think the "easiest" solution is altering the SB hulls and possibly adjusting the resource formula.

For CA going on the time travel theory, maybe they can only send through microscopic things like bacteria or non-physical things like radio waves? so they colonize the planet, send bacteria back in time, this then creates a parrelle world where the enviroment is perfect for them. they then are shifted to that reality and the planet is perfect. upon invasion they send a signal to the previous them to cancle the terraforming, thus it seems to be undone, this has the effect of shifting them back to the original timeline/parrellel world where nothing happened.