Have done the Med several times in a variety of itinerary combinations. Am doing it again this summer from Venice to Athens on the Grand, June 9.
Here are my thoughts, definitely take excursions if possible. As said, alot tend to pack a full day, but not always necessary.
In Naples, Pompeii in the morning, then back to the ship for lunch, then Herculaneum in the afternoon. Doing that again this summer.
Athens, at minimum, the 1/2 day to the Acropolis, Platka, etc. However, I've been to Cape Sounion for Poisedons Temple and it is a most beautiful spot, if you don't mind a full day, as they have one that combines both.
Kusadasi, of course, Ephesus is the #1 tour here, not a full day stop. If you have never been do the St. Johns Basicallica in combo with the Ephesus tour. I am going to Epheses (been before) but on the tour that has the Terrace Houses. Last time I was there, they were just excavating them.
Istanbul, most definitely want to do the Mosques, and Topkapki. Then maybe head off on your own to the bazaar.
Civatevecchia, do an all day Rome.
Livorno, since you are close, it'd be a shame not to see Pisa and Florence, the all day combo is the best option here.
Mykonos, never been.
Venice, we are going in early, but taking the Doge palace and San Marco tour since they'll have the tickets.
Any questions specifically, ask away.
When are you sailing?