Would like help with our Greek island itinerary.

I do not believe there are nonstops between Zakynthos and Crete ... you will have to change planes in Athens.

In 3 weeks, you can't really do more than 5 islands if you want to have 2-3 days in Athens at the end (and that really should be part of your trip -- its museums have the greatest treasures from all islands, except Crete). No point in picking & choosing among your random island list ... that would require doing a mini-guidebook describing highlights of each, i.e., Greece 101 ... it would help a lot if you'd spend 30-60 minutes browsing thru a guidebook yourself, (you can do this Free at Barnes & Noble or your local library), deciding which appeals most, rather than counting on us for all the backgrounding. A good (and candid) guidebook, such as Rough Guide to Greece, will explain the difference between one's experience at the height of high season (July-Aug) and distinctly off-season (end of Sept) ... some of these islands can be VERY quiet by Sept 30, things closed up... one of them is really 99% Greek, and not that welcoming to nonGreeks in my experience...

To get you started, here's a good map of Greece & islands http://www.explorecrete.com/crete-maps/images/greece.gif (Click to enlarge); This ferry map http://www.greeceathensaegeaninfo.com/ferry-info-greece/greek-islands-ferry-chart.htm -- while outdated, and frequency of service applies only to high season --- at least shows the basics of ferry networks, to show where you'd have to start, and where to go, to avoid backtracking.

PS: Samos is not anywhere near the cyclades... it is a 30-minute ferry ride to Turkey.

So ‘Sky Express’ actually has a non-stop flight from Zakynthos to Crete only on Fridays and Sundays. As I recall it’s the only direct flight from the Ionians. Athens will not be part of the trip since we’ve been before. The islands on the list were made after using guidebooks and doing research the past week(I do this kind of trip planning to Europe several time per year). The islands I'm considering can be directly linked, and although out of the way, I was considering Samos for the sake of diverseness. Thank you for linking the map but I just help solidifying my itenerary at this point...

Edit: current itinerary:

Mykonos 3 nights
Syros 2 nights
Naxos 4 nights
Santorini 2 nights
Crete 5 nights
Kefalonia 4 nights

Here us a link to the available Greek ferry routes. Expect somewhat reduced schedules the end of September.
http://www.greeceathensaegeaninfo.com/ferry-info-greece/greek-islands-ferry-chart.htm

That list looks do-able if the ferries work out... Syros is worth it for 1 night for the remarkable town "square" mainly... I would just say that this is the 99% Greek isle and you may feel a bit "left out" ... I was there with a greek family once, and once with an american, what a difference. Also, in terms of the "beauty" you list, as far as terrain or beaches, nothing notable. If ita port-town square is not on your bucket list, you might consider substituting one of those 2 other islands because of their scenic diversity/beauty -- Folegandros, just for its remarkable Chora (recommended hotel Anemousa on cliff edge) or Amorgos (recommend Aegali rather than Katapola)) Either one would fit into a ferry sequence between Naxos and Santorini.

As for Crete, you will need to ferry into Heraklion, but see if you can fly OUT of Chania... avoids backtracking.