I managed to unite the Byzantine Empire with the Bulgarian Empire through marriage, which made me think about the most historic outcome. Do you think in such a situation Bulgaria would be reincorporated, or remain as a separate title? There's no event to shift it back into Byzantium, unlike Rum.
My issues so far:
It doesn't seem possible to declare war on the Ecumenical Patriarchy or Miaphysite Papacy for Hagia Sophia or Alexandria, which makes fully controlling those provinces impossible.
Byzantium can usurp Rum.
Bulgarian Unrest popped up in a few provinces for me after I inherited the Bulgarian Empire.
Probably a vanilla issue, but when revoking titles from a duke with one holding as Byzantium, it wastes the traitor revocation permission on the duchy. Desired: Revoke duchy with administration permission, revoke country with traitor permission.
Pisa and Genoa hang around forever as titles even if they lose all their holdings in vassalage to a count.
IMO Knights Templar and Knights Hospitaller should be at least de jure Jerusalem, maybe even made to swear fealty on creation. Currently, they always join independence factions, which is extremely silly.