I have been to Greece four times. The first time I flew into Athens and did not go to any of the islands except for a one day trip to the three nearby islands to Athens.
Since then I have visited Greece three times on cruises. A cruise is a great way to see the islands, but you need more time in Athens than one day.
The weather is still pretty warm in October in Greece. We visited Athens and Mykonos while on a cruise in early October. Temps were up to low 80degrees F.
Athens still has a lot to see, but the city has gone downhill since the economic problems in Greece. Still, the Acropolis is amazing and there are great museums there such as the New Acropolis Museum and Archaeological Museum.
Dephi is worth a visit, as is Corinth and Sounion.
As for the islands, Santorini is magical. Mykonos is nice. I only had one day in Crete to see Knossos, and would love to spend more time there. Corfu was great, but it is on the NW corner of the country.
I would spend 2-3 days in Athens and try to find a cruise to visit as many island as you can. Also, haven't been to Rhodes, but it is good as well.