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.
This describes every realm I've ever played in except Tara. Seriously, do you think Morek is a monolithic bloc with an iron-fisted dictator? Then you're wildly mistaken about how it works and why it's been successful.
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..
A soft limit on realms size already exists, in that the acceptable tax rate is a function of size and distance from the capital. I think it's a good thing that this exists, but it should not be overdone. In particular, it should never be more profitable for a realm to shrink all else being equal. This is something that was sometimes the case with the old estate system, and honestly a great success of the new one in my opinion.
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.
I like these ideas, in that I like to see them implemented in the game by the players, but I think most of them already are.
Appointing another nations ruler should never be done game-mechanically, otherwise he isn't called a sovereign, he's a Duke and you come back to square one. However you can bully another realm to replace their current ruler by your favorite one. I've seen it done before.
You can control another realm's foreign relation by forcing them to sign a federation with you. That way, they need to follow your foreign relations or you'll automatically declare war on them. Of course, if in time the balance of power shifts, then it's not clear anymore which realm is the vassal: see Astrum/Caerwyn.
As for automatic tribute collection, I have nothing against it and I think it would be nice to have, but as has been pointed out I doubt it would solve all the things you want changed.
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.
What makes you think that vassals going against their Overlord's will would be more common than Dukes seceding are today?
