Which area of modern Greece, proceeded in preparation for statehood (independance), that was cancelled, in later stages?

Crete was autonomous, though the Cretans always intended union with Greece as far as I can tell. Samos was autonomous as well, though I have no reason to think they intended statehood.

There was a very short lived Provisional Government of Western Thrace, set up in the aftermath of the Balkan Wars, to try and prevent a Bulgarian takeover.

Outside of modern Greece, there was talk of an independent Pontic republic, and of an autonomous Greek republic in Southern Russia.