One thing to keep in mind is that there are 3 states to an SCL, even though there are only 2 effective ones right now.
In my previous game (a few patches ago but I don't think these have been touched) destroying the AI command center in the system is all it took, you did not have to actually build a human command center to get the AIP reduction.
I had two of the SCL's 'freed' this way, the systems they were in were neutral but they were still reducing my AIP.
So, change them up so that freeing the SCL gives a small bonus and capturing the SCL gives a bigger one.
What about changing SCLs to +1/AIP if held by AI, -1/AIP if in a neutral system and -4 AIP if captured by humans? (The human captured version would need a -15 or -20 AIP penalty if destroyed to avoid making it too easy to cheese.)
That means you need to hold the system to really get the benefits, but holding more then 2 (3 if the RNG likes you) SCLs would make your defensive options harder. (Assuming 80 planet map anyway.)
I also like the idea of making it -2/+1 AIP so the floor does keep increasing, again to prevent them from being too powerful.
Some thoughts anyawy.
D.