When we visited Sicily, it was with Oceania and we docked at Naxos. I had a hard time finding local tour guides and ended up doing a shore excursion to Mt. Etna...I was not that impressed. Wish I'd visited Taormina instead.
In Rhodes, also with Oceania, we docked right near the main gate to Rhodes Town...We took the shore excursion to Lindos in the morning and then just walked Rhodes on our own in the afternoon...If I did it over again, I'd skip Lindos and just spend all of my time in Rhodes--really charming and picturesque town.
I've been to Kusadasi twice...and both times, booked private tour through Ekol Travel...Their prices, even on a tour for two, worked out better than the ship's offerings...guides were great and we saw an awful lot...
First time, we did a full day tour to Miletus, Didyma and Ephesus--a lot more than one sees on any of the ship's excursions...Second time, we had a shorter day, so we just did a tour of Ephesus INCLUDING THE TERRACE HOUSES...definitely don't miss these...fantastic archaeologiic excavation...I highly recomend Ekol...
Good luck...