Missed a few things in this dev diary.
1) Cultural differences. It feels like assimilating people of Novgorod by Moscow should be easier comparing to assimilating Moscow people by Poland. The more differences nations have - the more difficult, risky, costly and time consuming assimilating should be. Also, it would be logical, if level of support of rebels depends on these cultural differences.
2) Vassal system. There was zero mentioning of it, but for me it is the key feature which adds depth to conquering countries. Also it feels like an answer to a problem of fast but successful invasions. If you've just swallowed whole country but don't have resources to assimilate people or to crush the riot - you could probably start negotiations with leader of riot. If negotiations go well, your kingdom will have some more independent than usual, but they will be peaceful. I think ideally conditions of vassal oath should depend on how strong position rebels have.