Here's a few suggestions:
RELIGION
-The "Total Depravity" Christian sect should be renamed to Augustinian or Hyperaugustinian; the Total Depravity name seems to suggest depravity is celebrated by them (which some Christian sects of the time actually did)
-"Ebionite" should be a Jewish sect; the Ebionites held to the Mosaic Covenant and laws, considered Jesus a prophet rather than the son of God, consider the apostle Paul to be an apostate, and some scholars claim to be one of the inspirations for Islam. Psilanthropism should merge with Ebionite for their similar view of Jesus.
-Another Jewish sect should be called "Nazarene", which like the Ebionites held to the Mosaic Covenant, but did consider Jesus to be the son of God, sided with Paul in the Council of Jerusalem, and believed in salvation through faith instead of salvation through works.
-I don't think "Kartvelian" should be a Christian sect; the Georgian patriarchates had no theological disagreements with Constantinople at the time.
-Since the Aquileians tried to reconcile Chalcedonians with Miaphysites, I believe the religion is redundant with Monothelitism (which was the same kind of conciliatory movement) being in the base game.
-Eutychanism and Apollinarism are Monophysite, and can therefore be considered redundant.
-"Abadite"is just another name for "Ibadi". Likewise, "Khawariji" is just another name for "Kharijite".
MAP CHANGES
-In order to accomodate the Sahara situation and bring it closer to CKII vanilla map standards, I think the Gaetulian and Garamantian tribes should be squished into a 1-province tall horizontal string of provinces, but each of those provinces should have 6 holdings to represent their wealth. An event or series of events related to the drying of the Sahara could then cut the number of holdings per province to 1 or 2.
-The Arabian Peninsula also deserves a province count reduction and a few more wastelands. Maybe even turning the Tribal characters into Nomadic ones.
-Iceland should be united under a Papar theocracy, but also receive some kind of massive income and levy nerf, to emphasize the fact that it was barely populated, if any.
THE DONATION OF PEPIN
Trigger: The Patriarch of Rome is landless, he is not a vassal of the ERE, and the ERE does not hold any province in the Exarchate of Ravenna.
The Patriarch of Rome can then get an inheritable claim on the provinces of the Exarchate of Ravenna, and ask any Nicene king to go to war to reconquer them. If he accepts and wins the war, the Pope gets the Exarchate, which becomes the Papal States and the king gets an alliance with the Pope, a massive piety boost and temple vassal opinion, a coronation (if he hasn't had one) and a diplomacy boost. This would also be a great time for Catholicism to spawn and convert all Nicene rulers and territories in the lands under the jurisdiction of the Patriarchate of Rome to Catholicism.
GOVERNMENT
CKII Imperial succession for Roman and Sub-Roman kingdoms.