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Tentative Greece Itinerary - with questions -- feedback wanted!

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I'm getting ready to purchase tickets for my trip next September and would like to try to get the itinerary down so that it coordinates as well as possible with the transportation. I'm planning to leave Thurs Sept 15 (arrive Fri Sept 16) and return home from Athens Sunday Oct 2. I'm looking at both Continental and Delta for direct flights from either JFK or Newark to Athens. I'm leaning toward the Continental flight because it arrives at 10:20am while the Delta arrives at 9:20am. Any opinions over preferred airline?

I have 16 nights in Greece, and my ideal itinerary is the following (details not included here):
Arrive Athens, fly to Chania/Crete.
Days 1-6 Crete
Days 7-9 Santorini
Days 10-13 Naxos
Day 14 (flight back to Athens) Delphi
Days 15-16 - Athens

My big concern is the long layover at Athens airport upon arrival. The earliest flight to Chania is at 14:20 on Aegean, and the one on Olympic Air is 2 hours later, which means there's a 4-5 hour wait at Athens airport. Overall, I do like the idea of flying directly to Crete on day 1, but I'm frustrated with what feels like a waste of time at the beginning, especially when we're struggling with jet lag. There are earlier flights to Heraklion, but that seems silly to do, since I do want to end up in Chania -- unless I need to stay in motion rather than sitting for several hours.

So to maximize our time and to take advantage of that post-flight adrenaline, I've been toying with alternatives. One possibility is going to Athens for the first night, then driving to Delphi for the 2nd night. Or even driving to Delphi upon arrival and returning to the airport the next day to fly to Chania -- although that seems like pushing it, considering the jet lag. Still, going directly to Delphi keeps to my overall itinerary without having to change the allocation of days, and gives us the flexibility of returning to the airport to take any of the flights to Chania we want. Still, my instinct tells me this is too much to do upon arrival.

So, if I stick to the above allocation of days (which I really like), and I decide to go to Athens on day 1, and Delphi on day 2, then I end up with only 1 day in Athens at the end, which seems too choppy. Or, if I want to end up with 2 days in Athens at the end, I have to sacrifice a day from one of the other locations, and I'm reluctant to do that.

So, my Fodors Greek travel specialist friends, what do I do? Do I just accept that first day at the airport as part of the travel compromise? I suspect that's what I'll end up doing, although it bugs me no end -- or is there an alternative itinerary that would work and still include the above itinerary (more or less?). What do you recommend?

Many thanks to all of you -- your input is greatly appreciated.

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