How would you create an itinerary? We will be going mid May and probably will skip Athens and fly directly from London. Where should we start? finish? How would you divide the time?
If you're flying direct the most logical route would be London>Crete>Santorini>Naxos, and after Naxos you'd return by ferry to Santorini or Crete the night before your flight home. Ferry Schedules: http://www.gtp.gr and http://www.openseas.gr/en/index.html
Not knowing how much time you have in Greece prevents me from making suggestions on how to divide your time. As a general rule I usually suggest a minimum of 4 nights on any island, but Crete really takes a minimum of a week with a rental car just to barely scratch the surface.
Given we have about 2 weeks would it be a better idea to just spend time on Crete and Santorini or visit Naxos during that time? Would another island besides Naxos be a good idea? It's half a day from Naxos back to Crete....worth it?
Paros is also close to Naxos so it would be a good choice as well. If it were me I'd spend a week on Crete and a week on Santorini.
Mid May is still early in the Greek holiday season. Personally, I would skip Santorini as it's over-priced, over busy and over-rated. Crete would be a good option. May is a better time to see Athens than in the summer when it's too hot, but your call depending on what you are interested in.
Not sure why you want to avoid Athens. Have you been there before? If not then if you don't go you'll miss some of the best world-class archeological sites and museums in the world! Then there is the Plaka, Monistiraki Sq., the Central Markets on Athinas St., Anafiotika (the Greek "island") on the north side of the Acropolis, changing of the guards, the Psiri District, numerous restaurants and tavernas serving real Greek food at very reasonable prices and so much more. Many people seem to think Athens is worth a visit . . . I disagree.