If it makes you feel better, I'm having the same problem. I allude to an alien race, and I never get inside their heads (so far), and this can be a grave mistake. I think all antags must be drawn as completely as the protags--given motivation, some type of flaw, sympathy, intelligence--all the elements of a 3-D persona. As it is, I've left them hanging out there as a mysterious presence, but they are responsible for heinous crimes and butchering. At the least, my bad guys are weak and two-dimensional. It is easy to correct however, by just giving them their own chapters, as Asimov did in The Gods Themselves.
Tri