The First Emperor had the idea to send out ships which were Mobile Robotic Construction Yards (MeRCY). They would construct a flotilla in transit in the last few years before arrival in the new system, giving them essentially new ships on arrival.
The new empire was called the Wavefront Empire, as it expanded in a wave front from the initial source, the capital. The MeRCYs dropped into their new system, the system was conquered, the MeRCY created a copy of itself and a new force was raised and trained in the capital, and everything was sent off to the next system, where the process was repeated.
The trouble came because the people of the capital were a limited commodity. They were thoroughly indoctrinated in the way of the Empire, but there were only so many of them. Eventually, as the empire expanded, important systems nearer the heart began filling military slots with locals, making them more responsive to local needs than Imperial needs. The assault forces began to be raised in long-conquered back areas of the Empire.
The longer a system was in the Wavefront Empire, the more it was trusted, all things being equal. The more it was trusted, the less brutal the occupying force, and thus the more potential for hidden agencies and corruption. Bits of the Empire began breaking away. Situation now - Empire trying to keep central concepts going, while empire continues to decentralize.