They may be similar in that they are both province-based RTS-with-pause 4X games that feature lots of conquest, but they also differ significantly in a lot of core mechanics. For example, CK2 is supposed to be a primarily character/dynasty driven game, and for that, a country-based coalition mechanic would look misplaced even if it was well implemented (which the new BadBoy system obviously isn't).
One of the initial design conceits was that the primary threats to outward expansion ought to come from an inherent instability of large empires; obviously the current designers think that the exact opposite should be the case.
I would say the problems began when Temporary Revolt titles were introduced in RoI. Prior to this when your vassals revolted they revolted as a group of allies, each with their entire levy and retinue, and they could call in other vassals as allies. This meant that a revolt which started out relatively small could snowball and end up including everyone, gradually stripping you of troops and revenue.
Added to this you have to worry about outside forces as other realms, particularly of a different religion, can gobble up entire kingdoms by fighting the individual vassals, I once ate most of the Holy land like this.
Now the faction fires and forms a new realm, with levy laws that limit the amount of troops the revolt leader can call on. They also tend to clump into bigger armies meaning that you can strike and defeat them more easily because rather than chase six to ten stacks you're only facing two or three.
From a gameplay perspective this makes it much easier for the player, and you're only likely to lose one Duchy to enemies outside the realm rather than three or four. I think the driving force behind the change was the player's ability to exploit this mechanic to rapidly expand when a neighbour was in Civil War, which is historically accurate, but the player was inevitably better at exploiting the opportunity whilst keeping their own realm together than the AI.
Anyway, since these temporary faction titles came along realm stability hasn't been a big problem once you got your retinue and demesne up together - it's only a problem initially because you haven't built many upgrades in your capital, saved any gold or built any retinues. Conclave seems like an attempt to add more instability into the system, something else the player needs to juggle but people are already finding that the Council is quite easy to game because they are the only people who vote now and you get to choose who they are.
Hence, I suspect, the new bad-boy mechanic and the reduction in the demesne limit.