First and foremost you need to be able to demoslish a economic/manufacturing etc capital. It's just flat out silly that once you put one down it'st here forever. Secondly when you conquer a planet that has one of these it should be destroyed automaticly. I just capture a run 4 world of the AI's and found out that one of the 3 buildings was an economic capital (don't ask me why the AI put it on that worthless rock). This happened before I had build my own economic capital and guess what I can't do now? So I'm forever stuck with this worthless economic capital on a size 4 world because I can't tear it down.
Nevermind that if you do have the capital already when you take another one over that gives you 2 + capitals of the same type.