I think we need to revist how Estates and other issues related to it work - the mistake I think in the changes made, as poined out already, is that to "encourage" desired behaviours huge negative effects were applied to things. Whether it was TMP or Estates, the failure is that negative punishment is used. Not getting Knights? BAM bad things happen. Not fighting wars? BAM bad things happen.
This is the wrong mentality to be enforcing - we should be reenforcing the desired effects by providing positive things when you have knights and war. Taking over regions becomes extremely difficult because the negatives applied to them due to the inability to get food, knights, lords, and a duchy given to them. Much like holding onto any region - it becomes a fight just to manage the region with police work and courtier work.
To make this easier - and to encourage more war and expansion (along with smaller realms being viable again) we need to place positive benefits to having Lords, Knights, Duchies etc applied to a region - rather than negatives (which are what happen when you lack them, and most Realms do).
Estates should provide bonuses to the region's stats, rather than be required to KEEP the region stable. Duchy allegiances could provide control, loyalty, production, etc style bonuses (perhaps chosen by the Duke or based on the City/Ducal centre type). Perhaps Estates allow for higher taxes to be extracted without a negative influence? Or reduce the upkeep of buildings, or the cost to construct new buildings? There are a large number of in game mechanics that Estates could provide as bonuses to a region where they are - Ducal Knight Estates could even be created to give Duchy wide bonuses. This would make having Ducal knights something desirable. Estates could influence religious beliefs, effect TO functions, and even increase the range/weapon/armour of units recruited from them (by small amounts obviously). Increase wood/metal etc production for when those are implemented.
The key here is to make having Knights and Estates beneficial to a region, something the players will WANT to have, but that will not destroy a Realm if they don't have enough knights (or lose players to attrition).
Obviously though there would be diminishing returns - having one estate supporting something would provide good effects, but as you stack the same type of estate you see a smaller and smaller gain. This would encourage diversity and provide a wider range of uses for Estates.
Regardless - the idea here is that too many of the in game mechanics punish - reducing the enjoyability of the game and making players focus on meeting game mechanic requirements (which is tedious and boring), rather than focus on other players and the enjoyability of the game.