Okay, here is my new suggestion for how the new "Crystal" mechanic should work.
Instead of calling it Crystal, the new resource is instead Captured AI Technology called Cynetic. Cynetic is drawn by nodes throughout the galaxy (on specific planets) directly from the AI Hive Mind, so accessing this sacred technology makes the AI VERY angry.
Cynetic is an indestructible, infinite resource, but it harvests very slowly. In addition, the longer you harvest said resource, the more dangerous the AI's response gets on that planet. For that reason, the player has the option of ignoring the resource entirely (and not harvesting it), as to not unnecessarily incite the AI's wrath.
To use this resource, there are special capturable "Cynetic Fabs" and "Cynetic Builders" scattered across the galaxy. The Cynetic Builder is like the one Keith talked about, that gives you a small supply of turrets, shields, and such, and can build things out of supply. The Cynetic Fabs are just like regular Fabs, so they give a random MKV Fleet or Starship, but they use Cynetic Research instead of M+C.
As I mentioned before, the AI's response to this "Cynetic Resource Hacking" operates on a planet by planet basis. The more Cynetic you have harvested from a specific planet, and the higher your AIP, the more severe the response will be.
Here is how the punishment works:
1) The AI is more likely to attack planets which are harvesting Cynetic.
2) When the AI destroys the Orbital Command Station on a planet that has been harvesting Cynetic, it begins to build its own "Stronghold" on that planet, to prevent you from recapturing it and continuing to harvest this secret resource.
3) The Battlements it will build on a neutral planet (that was harvesting Cynetic) are based on how much Cynetic you harvested, and how high your AIP is. If both of those are high, you'll be in for a pretty bad time.
There are different "categories" of the AI Centerpiece Stronghold Structure it builds on an ex-allied planet. These get progressively nastier.
A) "Normal" Stronghold - As the name says, this is nothing too special. It's just the regular Stronghold type that the AI builds one "low-threat" Cynetic-harvested planets.
B) "Rally" Stronghold - Like the Normal Stronghold, but also continual reinforces the planet with new units every few seconds until destroyed. Has the potential of making a massive fleet outside the player's base.
C) "Attrition" Stronghold - Like the name says, attritions every enemy ship on the planet, making it tough to take down.
D) "Cloaked" Stronghold - Cloaks every enemy ship on the planet, meaning you have to somehow destroy it before you can even start firing on every other threat.
E) "Revenge" Stronghold - Begins building a Nuke to use on a nearby player planet unless destroyed in time.
These are just some ideas of the types of Strongholds the AI may build.
In addition to the "Centerpiece" Stronghold building, the AI will also begin to build "Guard Posts" just as if it were a regular planet. These Guard Posts will count as supply, and AI reinforcements can spawn here. Unlike regular AI planets however, Stronghold planets will continue to build Guard Posts until the player comes and wipes it out. "Stronghold" Planets can also spawn Guardians as well.
As I said before, the "pain" inflicted on the player in these scenarios is completely OPTIONAL. If they choose to simply not harvest Cynetic, the AI will not respond with this kind of tactic. However, should the player CHOOSE to use this resource to bolster his forces, he better protect his planets damn well