Of the above groups the Dodecanese probably constitute the best opportunity to mix islands between groups. You could, for example, take the Blue Star Ferries and map an island-hopping route that essentially heads in the same direction. In this way you could take in some of the Cyclades – Syros, Mykonos, Patmos, Naxos and some of the Dodecanese – Patmos, Leros, Kos, Chalki, and Rhodes – without any backtracking. Hellenic Seaways is another major ferry company whose routes you may want to explore.
The United States, Australia, and to a lesser extent Brazil, Mexico, India, the United Kingdom, and Japan have "deregulated" their airlines. In the past, these governments dictated airfares, route networks, and other operational requirements for each airline. Since deregulation, airlines have been largely free to negotiate their own operating arrangements with different airports, enter and exit routes easily, and to levy airfares and supply flights according to market demand. The entry barriers for new airlines are lower in a deregulated market, and so the U.S. has seen hundreds of airlines start up (sometimes for only a brief operating period). This has produced far greater competition than before deregulation in most markets. The added competition, together with pricing freedom, means that new entrants often take market share with highly reduced rates that, to a limited degree, full service airlines must match. This is a major constraint on profitability for established carriers, which tend to have a higher cost base.

Like Imperial Airways, Air France and KLM's early growth depended heavily on the needs to service links with far-flung colonial possessions (North Africa and Indochina for the French and the East Indies for the Dutch). France began an air mail service to Morocco in 1919 that was bought out in 1927, renamed Aéropostale, and injected with capital to become a major international carrier. In 1933, Aéropostale went bankrupt, was nationalized and merged into Air France.
Considering your interests (great food, hiking, beaches, nightlife unimportant) then Naxos should definitely be your other island. (And Naxos has many daily ferry connections with both Santorini and Athens.) Also, Athens needs at least one full day to explore so you should drop any thoughts about Delphi or Nafplio. Also, I would look into flights from Athens to Santorini on your night of arrival. If you could get to Santorini that night (and move your day in Athens to the end of your trip) you’d almost gain an entire day and could spend two nights on Naxos.
Airlines have substantial fixed and operating costs to establish and maintain air services: labor, fuel, airplanes, engines, spares and parts, IT services and networks, airport equipment, airport handling services, booking commissions, advertising, catering, training, aviation insurance and other costs. Thus all but a small percentage of the income from ticket sales is paid out to a wide variety of external providers or internal cost centers.