My personal suggestion would be to have a random chance of having an enclave stop by when you eliminate a command station. Sort of a risk/reward scenario there, which players generally like.
The other thing you could do is tie a random chance to getting an enclave, perhaps a roll every so many minutes, if you have researched the warp sensor or something like that. In other words, a function of knowledge. If you did this, I kind of think they should be tied into turrets somehow, since they are defensive in nature, and it would be an encouragement to research more turrets or different kinds of turrets.
Random chances to have one of these for doing something gives it a very gamey feel but also tied to achievement.
To prevent them from being overpowered, just make them one mark below the AI *or* build points towards a random Neinzul ship; have them build up like a carrier.
There are so many fun ways you could incorporate these.