Some of these may have been mentioned before, but here is what I would like to see (eventually):
1)In game dissolving of King and Emperor level titles. Either through some sort of war, faction or event. a) Faction - (especially if the liege has low claim to the title [4th in line, weak claim etc.] A faction that forces the break up of their liege's primary title, and all vassals become independent. b) If you have to posses more than half of the de jure territories to form/ usurp a title, shouldnt the reverse be true as well. If a king or emperor looses, lets say 80% of his de jure territory (or all) then the title is destroyed. This would prevent the kind of scenarios that are constantly seen in Spain, where through inheritance a Spanish ruler gains all of the surviving king titles, and yet looses his primary (such as the king of Castile only having Leon) c) a tribal invader takes all of your liege's primary provinces, your liege, and the capital of the realm, then said tribal leader can proceed to destroy the realm instead of becoming your new liege.
2)more vassal tiers. This may not happen, but its good to dream, adding in things like Arch/ Grand Duke, Marquis, Viscount and High King. It would let players with super Kingdoms and Duchies give their titles away without granting independence.
b) also included should be Viceroys. Sort of taking a page out of HoI's playbook, players with multiple King titles (or even more so Emperor's who control another de jure empire) can, as an alternative to giving away unwanted titles can appoint a vassal to rule a kingdom or group of kingdoms and basically let the AI handle ruling titles you don't want to deal with so you can focus else where.
3) more options when dealing with troublesome vassals. For example: crushing a independence or Coup d'etat faction should let you imprison all faction members, not just the one who started the faction, and let you punish the traitors with out penalty instead of letting them back in as if nothing happened. Same goes for punishing a vassal who murdered a family member. I would also enjoy allowing rulers to intervene in their vassals wars. I cant even begin to tell you how many times I've seen my expertly crafted realm fall apart thanks to vassals pressing claims (such as the king of Jerusalem taking Castile, use levies then spawn in Jerusalem instead of Spain). If we can't join the war, at least let us secretly support a vassal of our choice with 50 legions of our elite guard in order to end years of vassal in fighting thats preventing primogeniture.
4) Loyalist Factions
5) better family relations to prevent the constant King Leer scenarios.