There are two slightly different itineraries...and I don't know which one you've booked...So, here are some notes on all of the ports:
Rome: Try to fly in at least a couple of days early...so much to see here
Sicily (Messina): We took a shorex to Mt. Etna...not really all that exciting...probably should have visited Taormina
Athens (Piraeus): If it's your first visit, I'd recommend the Shorex that goes to the Acropolis and Cape Sounion...We did that on our second visit...Our third time, we hired a private guide for a tour of the Pelopenese (Mycenae, Epidaurus, etc.)--great archaeological stuff...but save that for a second trip.
Ephesus (Kusadasi): Skip the ship's excursions and contact a private guide...We've used Ekol Travel twice...lower priced than the shore excursions, even for two...and you'll see far more without the big bus tour...If you have a long day, they can do a tour to Miletus, Didyma and Ephesus...If the day isd shorter, just do Ephesus--and don't miss the Terrace Houses (not included on most big bus tours)..
Rhodes: We did a shorex to Lindos...would noty bother if we went again...Rhodes Town itself is more fascinating...Can be easily done on one's own if you want.
Santorini: We've done a Shorex to the winery, view point, etc. Half day tour is enough...maye the one to Oia--that's always popular...Next trip we rented a car and did Ancient Thira on our own...not an easy drive/hike...One good part abnout the shorexes is they take you up the mountain by bus and then give you a cable car ticket to go back to the tender pier on your own...
Mykonos: We just wandered the town on our own...a very laid back resort island...no tour really needed...
Naples: Do NOT miss Pompeii...One time we did the LONG Capri, Sorrento, Pompei shorex...VERY GOOD...We've also done the popular Amalfi Coast by private tour--nice, but it has its limits...and most private tours can not take you through Pompeii--requires a LICENSED guide...
Chania (Souda),Crete: We did a shorex to the Palace at Knossos--really the one thing to see on Crete...
Hope this helps...
Good luck...