There is a way to predict a Rouge Faction Base's layout
One must have a good amount of knowledge of each faction as well as each faction's past events and therefor which technology each faction introduced into the game
Hellhounds introduced shock technology into the game in Shockwave, so Hellhounds Bases will probably have things like shock turrets, tanks, and troopers. Other standard units being in the mix, of course.
Red Locust introduced drone silos, so higher level Red Locust bases will have drone silos
Note: This theory gets more and more obvious when you deal with higher level rouge bases.
(Death Metal Playing In The Background)
War Commander: Level 43
Vega Conflict: Level 65
Battle Pirates: Who cares?