Iconium renamed Konya if that hasn't already been suggested.
Smyrna going away... I'm not so sure with Rhodes and Canakkale going away but it could be renamed Izmir.
Canakkale going away seems ok. I would prefer Bursa if we kept anything there but probably more should be added to eastern Anatolia.
Isparata or Baris? I am not sure how strong either Byzantine or Seljuk hold was here in 1100. Might be better to be made as Antalya and be the southern Byzantine outpost while Trebizond is the northern.
Ahlat/Erzurum/Baghesh- one of those to represent ancient Armenia and the lands around Lake Van should be in.
Seabaste/Sivas- also good idea.
Those combined with the Tarsus/Sis split seems well enough to me.
Byzantines would lose Athens(merged with Corinth) Rhodes, and Canakkale compared to early era now. Byzantines could gain Antalya. Overall +1 if Antalya included.
EDIT- added map