Hi again, TravelMom --
Lots of good destination choices, sequence not quite so good. First-timers seem always decide to do Athens first, before checking on experience of others. Vets usually suggest going first to your FARTHEST destinations then working y our way back, and save your Athens time for the final days. This is particularly important on shorter trips, where every hour is precious. That's because you need to be in Athens the night before your homebound flight anyway -- it's too chancy to fly in just hours before an international flight. A glitch could mean you miss that homebound flight, at Great cost. Thus you'd be going in to Athens & checking in/out of hotels TWICE - u could lose half a day. We advise if possible that you get a domestic flight if available about 2 hours after you arrive ... then you can recover from jet-lag on an Island, SO much more relaxing... and by the time you return to Athens, you're hip to all the ways Greece operates, and can cope efficiently with a big bustling World Capital crammed with stuff to see & do.
Of course if you arrive at 7pm totally exhausted f rom a 3-plane 24-hour ordeal from California, you could stay at a modest hotel or B & B near the airport (NOT the pricey Sofitel that's the only one IN the airport), and just collapse for the night, and zip back in the AM for a bargain morning flight. That also works.
This islands-first advice even makes sense for longer trips if - as in your case - you're going in September. Fact is, many islands start to close down a bit as the month advances. Not Santorini or Mykonos of course (due to those @$#!! cruise ships), but smaller ones with fewer year-round residents; when the Summer Rush subsides, some places start to close, Greeks are thinking about gettng on with their own lives. This is particularly noticeable in enchanting smaller isles like Milos, Folegandros, Amorgos. Also, ferry schedules get less convenient by mid-month. So why not reverse the Order? Look at a map, here's a good online one, click to enlarge - http://www.explorecrete.com/crete-maps/images/greece.gif -- and think about a sequence like this.
CRETE - 5 Days -- For history/archeology buffs, the MotherLode!! And it's wonderful in September... Fly into CHANIA, spend 2 days around here, then rental car; head S toward Lybian Sea; Phaistos, drive N.E. thru wine country (whee!) then Knossos, Heraklion Museum, and Onwards! HEraklion has daily ferries to Santorini which is the handy connector-island
SANTORINI - 2 nights is enough for the Famous View, and for Akrotiri
AMORGOS - FOLEGANDROS? - 2 nights - pick one; small, charming delightful; I hve favorite places in eacvh
NAXOS - 5 DAYS Large year-round population, port town always vibrant; LOTS of ancient sites, etc etc Great landscapes too. Get there before it changes; I read an ugly rumor that airport's being enlarged.
ATHENS STOPOVER 1 nights -- Ferry or fly in, spend 1 night see a sight, arrange rental car, move on
DELPHI (1 night) -- Arrive afternoon, see Museum, do Ruins next AM before bus tours arrive, move on
NAFPLIO AREA -- 4 -- So many highlights! Nemea, Nafplio Old Town itself, Mycenae, Tiryns, Epidaurus, Asine ...
WEST?? -- 4-5 Mystra - Messine - Pylos (nearby is my secret Eden, Hotel Zoe in Gialova), Nestor's Palace, Olympia ... then a 5hour drive (modern road) around the left rim of Pelops on modern road, back to Athens
ATHENS - The wrap-up... 4-5 days: after 25 days immersed in Greek history & culture, Athens landmarks & museums will resonate SO much more for you, as a finale!