We had been to Kusadasi and Ephesus on a previous cruise and so spent our time wandering around the old town and the small island located near the ship. For a first visit I would definitely recommend a trip to both Ephesus and the Virgin Mary's house.
Rhodes is easily walked around on your own as it is within 'shouting' distance of the ship. In fact there are so many ancient sites that one visit is not sufficient. They have even discovered the remains of the old port which are currently being excavated. You can see these from the ships deck. You will need good walking shoes.
Again we did our own thing and spent all the time in Rhodes town - although if you have long enough you can get a local bus to Lindos. This would be a great deal cheaper than taking the ships tour.
In Athens we took our first tour - to ancient Corinth and the canal. We chose to do this as we had been to Athens at least twice before each time getting a taxi to the station and a train into the city. It is small enough to wander around.
Both in Ashdod and Haifa we took the ships tours as we were not sure of the security situation in Israel. We had a tour to Jerusalem and Bethlehem one day and to Nazareth and Galilee the next. They were both brilliant and the highlight of our trip. In Ashdod we also took the ships shuttle into the town but were very disappointed as there was not much there.
Again we really enjoyed Malta and will go again. We did our own thing and spent most of the time in Valetta which is a short walk up from the pier. Do not get a taxi as they want 10 euros for the half mile journey. Once a the main city gate you can easily get a local bus to almost any destination in Malta often for less than one euro. Gozo is hard to get to in the time available but most other places are relatively near to Valetta.
The city of Valetta is very easy to navigate and so interesting. There is history on every corner and the EU is putting in a great deal of money to restore many of the buildings. It was also the cheapest port of call for drinks and snacks.