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.

Ferries between Naxos and Milos don’t start until June 7th (one each way, every day after that). Ferries between Santorini and Milos start April 28th and there is one every day in each direction. And there are always ferries between Naxos and Santorini. So if the dates work I would fly to Santorini (the longest leg) then ferry to Milos then Naxos and back to Athens. But if you need to travel between Naxos and Milos before the 7th then ferry Athens to Milos to Santorini to Naxos and back to Athens.
I would recommend Naxos over Mykonos and with 12 days you could easily add Paros too. With Santorini, Paros, and Naxos you’ll get a good mix of different delights and some ferry island hopping too which is fun in itself. 1.5 days in Athens is perfect for most – 1 day for the Plaka, Parthenon, Acropolis Museum area; and a half-day to visit the Archaeological Museum which is a short drive or walk from the Plaka but hard to fit in one day along with the other sights.
With a history dating to the Stone Age, Hvar is as fascinating as it is beautiful. Thirteenth-century walls surround Hvar Town, with its red-tiled roofs, and the ancient stone ruins of Stari Grad Plain became a UNESCO World Heritage site in 2008. A jaunt to the interior reveals rugged mountains, lush vineyards and fragrant lavender fields. Embark on a boat trip on the Adriatic to snorkel, swim in sea caves, and wander secret beaches and seaside hamlets.
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