I have a number of critiques and questions. Mostly about Traits. Please do not take offense. I am honestly curious. I like most of your changes, but some of them bother me.
I thought early middle ages Christian religious leaders often had their own castles, levied taxes, and maintained military forces. I have read a number of texts in which it was expected that a Bishop would serve his nominal liege in times of war without making exception for Martial duties. What is the rationale that Bishops cannot be Marshals?
Why can Holy Wars only target counties and not duchies? I would have thought Holy Wars could target kingdoms or anything smaller given the nominal objective of reclaiming the Holy Land and rebuilding the Kingdom of Jerusalem.
You said Orthodox Christians can only declare war on Pagans. Did you mean Holy War?
Why can Muslims not declare Holy Wars against eastern branches of Christianity? Historically, Mehmed Osman II justified his drive to conquer Constantinople by stating that being a ghazi was a basic duty equivalent in importance to jihad. He even made it part of his title after succeeding in conquering Constantinople. In this sense, ghazi was an honorific title you gained for fighting on behalf of Islam in order to spread Islam. It was a major factor in the spread of Islam throughout the territory conquered by Mehmed Osman II.
Why does Arbitrary gain +2 Intrigue? I would assume Arbitrary would make someone more Random.
Why does Brave gain -2 Intrigue? What does being Brave have to do with Intrigue? I would assume Brave would make someone more likely to take the Center or Pursue in combat.
Why does Celibate gain +2 Learning? Someone who is Celibate could engage in almost any other activity more often, whether leading to Learning or otherwise.
Why does Content gain +5 Vassal Opinion? If I were a vassal, and my liege was Content, I would be annoyed as it would impede my ability to ascend the ranks of nobility. I would need to work around my liege as I could be certain he or she would never ascend any higher except by luck or circumstance. They would be a barrier to my progression.
Why does Craven gain +1 Diplomacy? I would assume that if you are a coward you are more likely to bend under pressure, whether martial or social. You would probably negotiate very poorly and cave to demands. The same question applies for gaining +1 Intrigue. You would break under pressure and admit to anything or reveal all of your secrets more easily were you Craven.
Why does Duelist gain -1% Defense? Dueling requires both offense and defense in equal measure.
Why does Drunkard gain +3% Damage? A Drunkard would presumably be ineffective and cause further losses or make hasty and irrational decisions.
Why does Envious gain +1% Damage? I would assume someone who is jealous would take greater chances. While this may result in +1% Damage, it would also probably result in an equal chance of something going wrong.
Why does Gardener gain +1 Intrigue? I do not see the rationale.
Why does Gluttonous gain +0.5 Health? If you enjoy eating and eat too much then you are probably in poor physical condition and your Health probably suffers. I would imagine that Gluttonous grants negative Health.
Why would a Hedonist gain +2 Intrigue? Hedonisim is pleasure for the sake of pleasure. I do not see the rationale.
Why does Slothful gain +10% Fertility? If you are lazy, I assume it also applies in bed. I have friends who unfortunately fall into this category. There were running jokes about their ability to reproduce.
Why does Temperate gain -5% Tax? If you are temperate you do not indulge to excess. You are probably better with your money because you do not drink too much, eat too much, smoke too much, etc. You keep your hobbies and vices in check. I would assume Temperate would increase Tax.
Why does Trusting gain +1% Retreat? I do not see the rationale.
Why does Ugly gain +3% Morale Offense? I would assume that inspiring soldiers to charge the enemy requires presence and charisma. If you lack these, in part because you are Ugly, how does this work? I would assume the opposite, that Ugly impairs Morale Offense and Morale Defense.
Tall grants +5 Opposite Sex Opinion. This would generally only work were you male. The same point stands for Powerful Voice. I think it is dangerous to make congenital Traits that are gender dependent.