The idea of capturing Structures, for me, just doesn't fit; however this is just my opinion. I hope other people will give their opinion about the idea.
The main reason I think it won't be a good idea (and hasn't been incorporated in OP2) is because the units are captured by reprogramming them (You might want to do some readings on Spider Units). It seems to me that capturing units boils down to doing a software override -- if I am allowed the term. However, Structures, unlike other movable units are operated by Humans.
A structure Factory for example requires 3 workers. In order to capture that structure, you will have to send a diplomat who will talk them out of working for their current colony, have a tube system ready to make the structure operational after secession from the former command center. OR you could send an army of "humanoid" or specially trained workers who will barge into the structure and kill everyone. But again, you will be wasting precious resources (Humans) and you will be taking Outpost 2 and 3 concept elsewhere (you can go play Commando to quench your thirst of capturing other buildings).
This seems to be a lot, is cumbersome and rather needless. Disabling the Structure would be easier to achieve, AND in OP2 you are already able to disable structures. You just have to EMP them or cut the tube that connects them to the CC.
I know a lot of us have thought about capturing structures, but the idea is just too cumbersome. Reusing an abandoned enemy structures seems, to me, to be a better idea.
P.S: topic is still open to refine ideas. If nothing is posted, it will be closed.