The Sith Empire is ruled, as the name states, by the Sith. To be Sith is to know that you are the master, and even the lowliest Sith is apprenticed to a Dark Lord. As you said, we're thousands of years and a completely different empire away from Thrawn. Sith seem to be almost completely above Imperial military orders and punishment. Is this a good system? No, probably not, since Sith tend to be haughty and power-mad anyway. But it's the system the Sith Empire uses. As for the various fleets, what would you like to see them being used as? They seem to do their job just fine in ship battles.