Is there a specific example you have in mind and would like to see reproduced in BM? From there, it may be easier to work out the mechanism to make it happen.
Think about the HRE or Medieval France in where the ruler did not directly control every territory, but through the feudal system had to share power with many other nobles instead.
My recommendation would be to limit the size of the realms and duchies so that those who want to control much can only do it indirectly. That together with a way to establish a link between the realms that is not annexation but gives some power over them (automatic tribute collection, limit/control their foreign relations, maybe even appoint their ruler) would diminish the amount of nearly constant hegemonic power centers that paralyze the game, giving way to more and smaller ones. And the more people you have in power the less easy it is to reach a consensus, and the more likely to trigger some conflict.
Think about it this way: If one's interest is to hold power being the sole royal duke of the realm is the best way to go, even better than being ruler. Now if you limit the size of the duchy you force the power-seeker to value more the crown, which can hold control over a larger area. If you limit the size of the realms and implement a vassalage-system between them you get a ruler who can control large extensions of lands only through proxies, having to trust them. Then you have a much higher conflict potential.
To simplify it: Rulers are playing something resembling Europa Universalis. I propose Crusader Kings.
You say rulers can already demand tribute and force vassalage? Yes, but why would they do that if they can simply control the lands directly?
