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.
I'm not saying there are no internal conflicts. What I would like is to see them involving more "foreigners". If you have several small realms it will be much more of a regional crisis than the attrition inside Morek between a Duke and his ruler.
If there are internal conflicts or not inside Morek didn't make any difference to Libero or Summerdale if they never knew about it, or if it never affected them.
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.
By the existence of Astrum and Morek it is clearly not enough. Almost-30-region realms should not be possible to maintain, IMO.
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 is a different case. In the old estate system there was a limit on how many
regions you could get, and your realm was unable to expand further if without enough nobles. Given that you can theoretically have a Duchy per region or more, and a Lord can also be a Duke, restricting the size of Duchies won't be a problem in that sense.
Restricting the size of realms goes tied with the vassal-system proposal. One cannot go without the other. So you
would be able to keep expanding, but just not directly.
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.
A vassal-system without a realm-size limitation makes no difference.
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.
Rulers are not necessarily sovereigns. In any case you can fight against the game mechanics to impose your will, but that doesn't make having the game mechanics to support it undesirable.
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.
And you are also forced to follow their foreign relations or you'll automatically declare war on each other, and on the other federated partners, messing things up.
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.
By itself alone, no. Together with the realm-size limitation yes. Or at least I think it would.
What makes you think that vassals going against their Overlord's will would be more common than Dukes seceding are today?
The messaging system is not limited by duchies, but by realms. If each duchy was a realm you'd have much smaller power groups, and the realm-nationalism we see now would be more duchy-focused.
It is much easier to oppose/hate foreign oppressors/enemies than it is to do it with native ones with which your communication is much greater. In general, naturally.
Check the newly-implemented Duchies map. Think about if all of those were mini-realms on their own, having to interact with each other. How much more dynamic would the politics be?