Vatican City would have to be in as an off-map state, as it is in Mod-33. It would add some flavor but I think that might better be done by coming up with a set of ministers for "International Community" Though it would have absolutely no effect on game play one might make the Pope a "Man of the People" Minister of Security for the International Community.
Taiwan is already in the game.
Hong Kong was leased by treaty from China and by treaty had to revert to Chinese control by 1997.
Okinawa and or Ryuku? No. Non-existent state. New Nations tried it and failed miserably at finding ministers.
Khanate Mongolia??? I think that is a special interest thing that could best be resolved by playing Mongolia, turning "tech team takeover on annexation" on, and adding cores by event. You can use the "steal_leader" command in your inc file for Mongolia to add a host of new leaders--suggest raiding the UPE and Turkestan (U35) files. You can also patch in the MEN ministers, giving them new numbers, into your ministers file and maybe do the same with their tech teams. Use your imagination. There's also a releasable Idel-Ural state (U11) that is quite strong.
East Timor is in the game already.
Acre? If this is what you mean by Acre you really lost me
http://en.wikipedia.org/wiki/Acre,_Israel
Crete and Sicily would IMO be most applicable in the event of a Soviet steamroller in Europe in which they controlled Greece and Italy but none of the islands. But that usually eventually becomes a Soviet world conquest. The biggest issue is this--how on earth would I find ministers for Crete or Sicily? I think the best idea would be a Mediterranean mega-nation based on Cyprus plus Malta. Then you just add Crete, Sicily and other Greek Islands to their claims. On the other hand you could always release "something" by just writing a custom event to release "European Union".