The ai logic seems odd(or at least exploitable) when there is no player built command center in a system. Take the following example, you clear out a border system, build a command center, harvesters, reactors and some turrets, then lose(or scrap) the command center. You are still get the main benefits from the system(resources/energy), but don't seem to have to worry about raids(since the computer sees the system as being neutral). Its basically a free warp jammer that instead of costing 20/20/30k and 5k knowledge, costs 16/16/2k(only real loss is loss of building ability, but a mobile builder can help here somewhat). Yeah you have to deal with wandering enemies, but if you are off the warpgate paths, most of them don't seem to bother at least your reactors which can turreted.
Short version, the ai should raid planets that you have harvesters and reactors on (at least, perhaps stardocks, etc. if we want to avoid other exploits with raiding), not only command centers.
This might not work as well on higher difficulties or against more aggressive ai types, but it still seems poor. Note this is 1.201.