There's an awful lot of island groups to explore and neither a cruise or following the main ferry routes is going to get you to them all in a less than a whole summer. Out favourites are the Cyclades (esp. Naoussa on Paros) followed by the Ionian. Normally we go somewhere in Greece at least once a year.

One compromise is to travel by ferry but book ahead into accommodation - there's plenty of net access or use a smartphone. You can get ferry tickets on demand at the terminals or from lots of the travel agencies in the resorts/ports.

A lot of the Aegean is very windy in high summer with the Meltemi blowing hard quite often. By the end of August we normally (but not always) find it is better and the days are still warm and it isn't dark too early. We find late Sept/Oct the days are too short and you start to find places closing - some as early as 1st Sept! Earlier in the year is nice but the Med hasn't warmed up.

Wherever you go you'll love it!
Yammas!