Overall I have to agree with you Bluebags, and I would have to say that the Byzantines should not be allowed to recapture so many if their take. Cities, once the Sultanate of Rum eventually collapses (which historically it did), what needs to happen is that the independent cities led behind be not touched by Roman influence.
As for the Fatimids, I think they are way to powerful. When you have a civ which lasts from 900 to 1500 AD, something has got to give. Plus if the human is playing an Egyptian civ, then this shouldn't happen, otherwise, the Fatimids should more often then not auto collapse to make way for the Ayyubids, who actually help threaten the Crusader states, therefore making more challenging for the player (if you are a Crusader). Something I don't like us the fact that people play as the Crusader civs and try to keep the Fatimids afloat so they don't collapse and spawn the Ayyubids, which I think is just wrong altogether, the Ayyubids really do need to spawn more often