I imagine this problem would be magnified tenfold with China. Although quite interesting, is the prospect of a foreign ruler remaining foreign, but delegating provincial rule to local Princes. Effectively no culture change would ever, ever happen, besides maybe the Emperor's culture moving to the capital. It would make succession explosive but you'd not have to bother with peasant revolts. You can either deal with anywhere around 2-3 centuries of peasant revolts and end up with an Empire of happy nobles of one culture and one people or compromise with an Empire of unhappy nobles but happy people or an Empire of unhappy people with happy nobles. It's usually better to either side with the people or replace them with your people, as nobles are fickle and unlikely to like you either way.
Historically, the Yuan Dynasty did the latter option, while the Manchu Dynasty did mostly the first option (though after a while they started employing Han nobility as well, just because they were running out of Manchus to give titles to -- it takes a LOT of people to administer an empire that damn big).
The Mongol
modus operandi was to leave the local government of a place mostly intact at the lower levels and just replace the top guy. Find the smartest, most respected local leaders, co-opt them with a mixture of rewards and threats, and let them run the day-to-day stuff. Keeps the locals happy, and cuts down on how many of your horde you need to leave behind to run the place.
The downside of this in China was that it tended to speed up the Sinicization process. The Manchu knew this, so they insisted on appointing Manchu nobles and keeping the Han a subservient class. The Yuan ruled for about 90 years. The Manchu, for about 270. So history seems to have spoken on which was more effective. But there's another factor -- religion.
There were a couple of *massive* revolts during the 1800s (the Taiping Rebellion and the Dushan Rebellion -- the Taiping Rebellion being estimated to have been one of the deadliest conflicts in human history) but in general, the Manchu Qing successfully used Confucianism to foster popular support. To that extent, Confucianism as a religion should have serious revolt-reducing benefits, but at the cost of technological progress (the emphasis on social order and orthodoxy also being responsible for centuries of technological stagnation). Taoism and Buddhism should be alternate options, with Buddhism already defined in the game as giving tech benefits. (The Yuan Mongols were Tibetan Buddhists and made Buddhism the state religion, building stupas all across China).
Not sure how Taoism should be handled -- it was never a state religion, and frequently when it showed up in Chinese politics, it was as the basis for popular rebellions like the Yellow Turbans. To some extent, it could almost be like a heresy of Confucianism (although as a Taoist myself, that is so laughably wrong...) with a stability/revolt malus, but I'm not sure what the benefit would be. Maybe an event chain to get super-statted characters, kind of like the Antichrist event chain for Christianity? That would actually be in keeping with Chinese popular mythology too, where Taoist rebels are often depicted as black magicians.
Something else interesting (and sort of occurs naturally in CK2 if you come to a royal/Imperial throne via the right kind of war) is that it was customary for a new dynasty to invest the dethroned Emperor from the old dynasty with a Ducal (公) title and fief. As it is now, if you usurp a title, the usurpee typically does keep their lower titles.