At first i thought it was a great idea, but then i changed my mind.
I think the planets on their own should all be the same. Or, at most have some special traits unrelated to AI.
It would be more logical to add different structures for those modifiers. For negative thats simple, and the structures can be either invincible, or cost AIP on kill like BHMs.
For positive its not as easy, but i guess you could make some hackable structures, so the player has to actually hack some structure to activate the bonus, or they could affect all surrounding planets so you have to capture them.
I find this one in particular to be intriguing, as it sounds like a smaller part of an overall ecosystem.
Story-wise, the systems serve no useful function for the AI whatsoever. They dont yield any resources, and all the production is done somewhere "outside".
And since the only purpose of those systems is securing defense against humans, different aspcets of defence are the the limit there.
Not like thats not enough though, the whole concept of some different key planets containing important things that have galaxy-wide effect would be cool. Right now the closest thing we have are CSGs, and the benefit they provide is really extremely simple.
I'm talking about different stuff like special structures that grant AI things like "power for AI home fotresses", "2x damage and armor on all core X posts", "Power on all MK X ion cannons", and so on. There are so many things to disable/cripple!