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We recently took a cruise in that area but from your list, we only visited Santorini. It is beautiful and in September the weather should be perfect. It was very hot when we went. The ship does not dock so you will be tendered. And I hope for your sake that yours is the only ship in port at that time. Only two ways to get up to beautiful Santorini. A small cable car which takes 36 persons at a time (6 cabins of 6) so the lines can be long. The other way is a 598 steps/donkey path (consequently not too clean) and can be very slippery. We learned the hard way because we had no patience to wait in the heat for the cable car to come down, and took the steps. Many people were slipping and sliding, even with good shoes. The more adventurous can rent a donkey to come down on the same path. Great shopping...lots of artsy glass, quite different from Venetian style. Many art galleries and sculptures. Jewellery is also beautiful.
We went on the Costa Victoria end of July on the same trip you are going on. Stopping in Sicily - a tour may be better say to Mount Etna, but we went into the town and found it to be very mediocre. Last year we stopped at Palermo and this year it was Catania, not much at all to be said about either port for shopping, you can walk to the town centre from the ship it is docked in port. Patmos and Mykonos were both absolutely lovely for 'souvenier shopping'. Mykonos has more individual shops along with souvenier shops, both worth going to as opposed to doing a tour and with both you had a tender boat take you to the shore, in Mykonos a coach was laid on to take you the mile into the harbour. Santorini is again a tender boat to take you to the shore,there is a cable car to take you up to the main village, better to take that than the donkey ride, because it is very steep and the donkey route is smelly, so i was told. A tour would be good for Santorini. But if you didn't want to go up to a village there is a handful of shops/cafes/bars just on the quayside. You dont have long in Santorini but long enough to shop. We went on a full day to tour Ephesus, dont bother, they take you to a carpet shop which is a waste of time. if you really want to see Ephesus thats fine but you dont have long to shop, maybe 20mins. and you are bothered by the street vendors all the time. Other passengers got a taxi into Izmir town from the port, where the ship docks and the driver took them shopping, a better thing to do from what we experienced. We didn't have a drinks package. Lovely ship, excellent crew, very good cabins and service and food. Enjoy!!