I don't mod for this game, so am not exactly aware of the limits and options for modding in CK2, but my suggestions are as follows:
With 3.0 a feature was added that would make your character fatter (or thinner) based on a trait, I assume this is some similar portrait-morph command, and might be usable for other purposes.
-Vampire / Werewolf, and 'Vampire Lord' portrait changes, if possible (Lich additionally)
A 'study dark seekrats' (not seriously named that) option, allows you to look into Lyncanthropy, Vampirism, Necromancy, Lichdom, etc. would (or should) be based on a combination of Religion (i.e. Daedric Cult), Traits (mainly negative traits associated with an immoral character, or otherwise is already one of the above), or perhaps added through a new group, comparable to the Devil Worshipers in the base-game, with this added to the Intrigue panel pertaining to them.
Vampire 'families', functioning similar to Secret-Religion Cults, and allowing you to seed the country sides with your spawn and supporters, with really powerful bonuses associated with being the Patriarch or Matriarch of the associated 'family' or 'clan'.
Equipment that can be purchased (or created for you), based on your rank, and what group you are in. I.e. Fighter's Guild would commission Banded Iron Armor, ready for obtaining for a (relatively) low purchase price, as long as you are above X rank; Mages Guild assembles Robes that increase Magicka Regen; Dark Brotherhood provides armor that increases Plot Power, Weapons that do so and grant other bonuses, etc.
'Dark Resurrection', I encountered a Dragon (that then randomly died of natural causes) in my recent EK play-through, among others, and found that it would be interesting if (assuming possible), characters, once dead, could be resurrected as mindless Thralls that serve and obey.