With regard to excursions offered by the cruise line, think about the following:
We've taken many, many cruises (including ones in the Med.). but rarely is one able to get off the ship for at least an hour (or two) after the arrival time. Your days might not be as long as you think.
In small places such as Malta, Mykonos, and others using a private guide or doing something on your own and getting back to the ship on time might not be a big risk. In places such as Athens, Istanbul, and Rome, it is a whole different set of circumstances. There can be traffic delays, train delays, as well as road construction delays
If you are on a ship excursion, the ship will wait for you. Not so if you are on your own or with a private guide. Three or four times we've seen people literally running along the pier as the ship departed. Yes, ship excursions do cost a bit more than doing it on your own or with a private guide. But they are a lot cheaper that getting yourself to the next port to catch up with the ship.
Our rule of thumb is "Can we get back to the port or tender dock by hoofing it?" Depending on what you plan is (and how far afield you plan to go), some places can be done on your own or with a private guide. In other places, the ship excursion will be a lot less stressful than doing it yourself.
Don't mean to sound like Debbie Downer, just offering some thoughts for consideration.
