A few questions

[caravel]

The landbridges will make all the difference, as they will prevent the AI getting cut off on the islands - so no more Byzantine reappearances on Crete with 10,000 men - and no port...

Without landbridges the islands are useless, in fact some of the islands are useless anyway such as Malta and Rhodes (all that they add is "flavour" and they may be worthwhile if you're adding crusader states factions to the game). I have removed those two and used the provinces elsewhere, but if you're keeping them the landbridges are a must - even if you still have shipping.