@Potential: The game crashed when I click start with the Potential; it can't even load with all that power. I don't remember how much power my OP Testrel had when it crashed, but I think it was some random number like 44.
@Ion Beams: They look to be the same for me. The Advanced Hacking System on my Frankenstein works like it always did, except now it is PURPLE!

Unfortunately, I ran into a few other problems that I still need to fix before releasing an update.
My A.H.S. uses a 1 length / 1 speed beam with 2 ion damage and 1 system damage. In order to pierce 1 layer of shield and still hit the system beneath, I had to set shield piercing to 2. During my recent test against 4 layers of shields, it would usually hit 3 times, leaving 1 shield layer left, but sometimes was capable of hitting a fourth time and completely removing the shield.
@Eight system cap: When including the subsystems, there appears to be a 12 system cap. My Frankenstein test started with nine systems and two subsystems. The upgrade screen UI only has 3 subsystem slots instead of 4. When I bought a subsystem, I couldn't find anymore stores that would include a system section. I don't know what would've happened if that store had offered both of the missing subsystems.
@Medbay/Clonebay: Assigning them to different rooms does not allow you to have both. It will remove the other one.
I feel like I'm forgetting something again...
