I think the Seljuks should start at war with the Fatimids from the start. IIRC, they were at war by 1066.
But then they'd be fighting two powers at once. That would make the Byzzies too powerful again.
They need more decadence, Sunni provinces, angrier vassals, and the lowest crown authority at game-start. Or, alternatively, keep them as they are but stop them from attacking Greece through some mechanism or other.
In fact, the latter would probably be the best choice. Maybe change the invasion+ Holy War CBs so that you have to have a direct land border with the duchy/kingdom to be invaded.