Having played a bit, I've come to the conclusion that the Subjugation and long-term tributary CB must be removed or its mechanic severely reevaluated. I would be fine with it being completely removed, or Subjugation should be limited in scope and granted only through a Mandate from the Emperor or the Shogun. Personally, I'd keep it only as a CB to unite a province if you are hold that province's shugo post, or upon the Shogun or the Emperor's command by event. This would make currying favour with the Court much more important - and interesting.
Starting at the MEIOU coup, independent realms are routinely and constantly involved in between 2-4 wars, not leaving them any time to recuperate before bigger neighbors (or the Shogunate) comes knocking on their door. Also this makes Alliances nigh-on useless as a bangwagoning tool against bigger daimyo, because you will constantly be asked to join your ally's war and if you do not send your troops you risk the AI breaking off your Alliance.
Also, I would remove the threat threshold alltogether for Defensive Pacts - if you are small enough and your neighbor is enormous, regardless of the threat you should be able to form a defensive coaliton with your other neighbors.