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.

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A complicating factor is that of origin-destination control ("O&D control"). Someone purchasing a ticket from Melbourne to Sydney (as an example) for A$200 is competing with someone else who wants to fly Melbourne to Los Angeles through Sydney on the same flight, and who is willing to pay A$1400. Should the airline prefer the $1400 passenger, or the $200 passenger plus a possible Sydney-Los Angeles passenger willing to pay $1300? Airlines have to make hundreds of thousands of similar pricing decisions daily.