It's up to you whether you book a tour from the ship. In Kusadasi it is well worth visiting Ephesus, the wonderfully preserved ancient city.You may well be able to book a trip on shore. I went on a trip organised by the ship and found it good value.
Athens is easy to do by yourself - walk to the metro, which was a pleasant walk taking 25 minutes. There is a good, safe sidewalk, and as long as you keep the water on your left and keep walking past all the ferry piers, you can’t miss seeing the escalator and overhead walkway that lead across the main street to the metro stop. Fare was 0.80 €, and the metro was very efficient since it is not affected by traffic. It takes about 20 minutes to get to Monasterion (Monasteraki) stop which is near Acropolis. 12€ combo ticket gets you into Roman Forum and acropolis. At 7 €, the National Archaeological Museum of Athens is an amazing bargain and this is at Viktoria metro stop.
My family are going on the same cruise. My 2 daughters aged 21 and 14 would like to visit a beach whilst in Crete but the organised excursion to a beach is £22.00 for 4 hours. Rather steep we thought. I'm sure we must be able to get a taxi from the port to a local beach. Could anyone recommend a nice beach close to the port which has watersports eg, banana boats, pedalos etc? Thank you.
Kusadasi - be adventurous and catch the only public bus to Ephesus - which is the local bus (its actually a large van) that runs from the bus station (which is on the other side of town from the outdoor bazaar) along the road down below Kusadasi. You have to get off at the small bus stop (a tiny kiosk) on the main road and than hike up about a mile to the entrance to the ruins. Keep in mind that the main entrance is at the top of the ruins (the furthest entrance from the main road) and than you walk downhill through the ruins and exit at the bottom. When you walk back to the main road you pick-up the return bus on the other side of the main road (there is another small kiosk).
I'm going on a similar cruise next May (Navigator of the Seas - same ports of call), as my father is elderly and can't walk too far, we prefer the organised tours - had anyone been to these destinations and can suggest tours we really shouldn't miss, it's difficult to choose from so many :o)