Last year we made the same cruise. We arrived in Athens a day early and were able to wander around the Plaka and have dinner at a scenic taverna that evening, spend the night, go on a city tour of Athens (including the Acropolis/Parthenon) that morning and then board the Windspirit after lunch. We had been told that was all we needed to do in order to see the best of Athens and I believe it. Some people on our cruise had spent more time there but they had used it as a base to travel to neighboring sites.
Some advice about the ports:
Mykonos: The tour to nearby Delos is worth it. Delos was revered by both the Greeks and the Romans as the birthplace of Apollo and served as a major trading port to several ancient civilizations. Wear sunscreen and a hat ---NO SHADE. The tour goes until lunchtime and you can either return to the ship for lunch or eat out. We had already decided to eat "local" whenever possible to get as much of the experience as possible (BTW the food on the ship is excellent). Afterwards, there is time to visit the shops or the beach; the ship doesn't sail until late.
Santorini: Because this route arrives here on Monday, the ruins at Akrotiri are closed. The only tour available takes you to the picturesque town of Ia (or Oia in some books). Visit the town on your own --- don't bother with the tour. This is one of the two big regrets of our cruise (the other was not staying longer in Istanbul). This tour took us to the highest point of the island, the Profitis Illas mountain, where you can see both sides of the island, which was not uninteresting but it was a big time-waster considering that the ship has to set sail at 4:30 pm in order to make Rhodes by the next morning (shortest port time on the cruise) By the time we arrived in Ia, we only had an hour and a half to see it. Another couple invited us to rent a taxi with them to go directly to Ia instead of the tour and we declined. Big mistake on our part; they had time to see the whole town and do some shopping as well.
Rhodes: We took the tour to the Acropolis at Lindos and enjoyed it. The tour guide was very knowledgeable about the history of the area and from what I heard later had good advice about places to eat and shop in the town after the tour. Once on our own, we paid the admission so we could walk on the top of the walls around the old fortress (again, no shade, need good sunscreen and a hat) and visited the "Palace of the Grand Master" at the fortress -- probably the worst of the sites we visited because the pamplet and the signs explained little about the displays and the docents (if you could call them that) just said "I don't know" about everything we asked. Perhaps they didn't speak English but if so, they were among the few people we met who didn't.
BTW: We shared Rhodes and Bodrum with the passengers on the sister ship Windstar (the Istanbul-to-Athens route). We didn't have many opportunities to interact with them, but it was neat to see the two ships side-by-side in the ports.
Bodrum: The most relaxing and longest tour of the cruise. We hesitated taking this tour because it takes up the whole time the ship is in port and is the most expensive but it was worth it. We were broken up into groups of only 10 and taken to the port-side Museum of Underwater Archeology. Very few of the artifacts there are reproductions and span several centuries and civilizations. Then, we were escorted on board a small sailboat (called a "gullet") and taken to a quiet cove where we were invited to change into bathing suits and swim (water was a little too cold for me though) and sunbathe while the crew fixed us a wonderful lunch of local dishes. We spent the rest of the day relaxing and sunning on the gullet. We needed that after 3 days of sight-seeing. When we got back to the ship, we were entertained by a troup of local dancers along with a belly dancer in the ship's lounge and then it was time for the pooldeck BBQ. Tons of fun and great food and dancing under the stars. We also got the see the Windstar put up her sails and head to Santorini; good picture taking opportunity since you can't really get a good picture of the Windspirit with sails up. Many of us agreed that this was the best day of our trip.
Kusadasi & Ephesus: Before starting the cruise we booked a tour from a local company called Byzance ( http://more.at/Byzance
) . We can't say enough great things about them and the tours they provided. Guide was waiting for us at the port, ready to begin our day. I requested that we try to avoid the ship's buses, and they did everything possible to make sure this occurred! It was a pleasure to enjoy the same places that the ship offered at our own pace, staying as long or as short as We wanted for a fraction of the cost! The fact that we were "alone" made it much more personalized.
On most of our tours, we had around 30 people and each and every one of them RAVED about the great time they had. It always seems there is usually someone who may have a concern or complaint, however this was not the case with Byzance. Our guide was very knowledgeable and friendly. We will most definitely use them on future cruises and from comments made from our group, I can assure you they will also!
The Sea Day: We needed this time off at this point. We were just about "ruin-ed out" and needed a break. We took the tour of the galley that the Chef offered and had massages in the beauty salon. The dinner that night included beef tenderloin and lamb chops --- both were excellent and we celebrated over a bottle of champagne our last evening on board with two other couples we had become fast friends with.
Istanbul: You will regret it as we did if you do not spend a couple of days here. We used Byzance here too. I could not be happier with the service we received from guide, I have never had a more positive experience with any company of any kind -- EVER! I don't know what more I could say. We had to leave very early the next morning after our arrival so we only had time to see the Blue Mosque and the Hagia Sophia and walk through a small part of the Grand Bazaar. That means we missed Topkapi Palace entirely (it takes 4-5 hours to tour properly) and several other places we wanted to see. This is definitely on our list of places we wish to re-visit one day.
I hope this helps anyone considering this cruise. It was the trip of a lifetime for us and we have wonderful memories of the people we met and places we visited.