We could always provide incentives for noble families to give up their control. Or rather, increase their responsibilities until they become weighty enough that the nobles in question no longer wish to deal with the hassle.
There is no hurry on this, so we could also simply make it very clear what is and what is not legally allowed for such nobles, then set the penalties for breaking those laws or exceeding the bounds on their authority to include loss of their hereditary positions. Then it would just be a matter of waiting for them to fuck up, because there would inevitably be some fuck ups every so often. In those cases, we move in and replace the ruling nobles with the already active Council. In this case, the Councils would serve as ever present reminders that we are simply waiting for the nobles to make a mess of things to give us an excuse to replace them.
Or we could require nobles who rule over a piece of land to pass an exam in order to maintain their control. Make it once a generation and applicable to an upcoming heir, with relevant tests of knowledge and character using a sentient Construct which can be guaranteed to be non-biased. If one fails the test, their house's nobility goes on probation and they get one more try in X years to requalify. If one fails
very badly, there is no probation and the loss is immediate. This sounds harsh, but it would be a good way to remove noble houses from control using a "fair" method, while also insuring that the heirs who will be taking such tests get the finest education and grounding in Imperial ethics money and paranoia can buy.
EDIT: Or,
@TalonofAnathrax, if we wish to maintain nobility as a ruling class, such exams could be used to determine likely candidates to replace those who fail in their duties.