Congratulations on your upcoming nuptials, and best wishes for a splendid honeymoon. We'd like to help you optimize your Greece visit, and you can make this possible by giving us more information, such as:
• Exactly how many days On the Ground? If you're leaving y our home on the 16th (and it may take up to 28 hours "clock time") and departing on the 28th, you actually have only 10 days, not 12. If you've booked your flight or have a good idea of what flight you'll book, please tell us what day AND time of day you'll arrive, ditto for departure. In a short trip every HOUR matters in planning.
• Where are you coming from? It's not dangerous to tell us which country -- and if from N. America, it matters whether it's East coast or west -- very different. This wil help us see how energetic vs. exhausted you'll be upon arrval, thus what is possible.
• Tell us WHY you're interested in Pelops, Mykonos or Crete: from your own research or "friends have told us"? Tell us a bit about the interests the 2 of you have: ancient sites? landscapes? night life? authentic foods, village life? Luxurious amenities, solitude?
My own preliminary thoughts (agreeing with several comments):
• Athens will be the liveliest venue, and a lot of fun in November so you should save 3 days for it, preferably at the end of your trip, UNLESS you arrive after a 25-hour journey, totally exhausted. Otherwise, the end-time is most efficient, since otherwise you must travel TWICE from Airport to central athens, check in/out of hotel Twice. In a short trip, to repeat, every hour matters.
• For 10-11 days, you really have time only for Athens, Santorini, and ONE other place. If it's CRETE, you'd need to fly to Chania upon arrive, spend 4 days (w rental car), ferry to Santorini for 3 days, then Athens for the end. If it's a Cycladic island, you should fly to Santorini, then ferry to NAXOS (which is right next to it, and has a large permanent population... stay right by the port town, and there will be some activities going on). Then fly back to Athens.
• My own personal suggestion would be: Fly to Santorini for 3 days -- Fly back to ATH airport, and rent a car and drive to NAFPLIO. Only 2+ hours away on the country's most modern multi-lane highway, This place is considered THE most beatiful "old Town" in all of Greece -- in fact, it's been called the "proposal capital of Greece," because so many men take sweethearts there for the Big Ask (including a friend of mine, who married a Greek; she said Yes). Nafplio is the favorite "3-day getaway" for savvy Athenians, so it's lively all year round .. and has lots of great dining, shops, etc. Also it's dead-center for Ancient history; famous sites surround it. This superb NONcommercial website http://www.visitnafplio.com tells all -- click on EVERY link, including directions to get there, and "really useful" (where to stay-eat-shop). I know the creator (a Scandinavian expat) and agree w. her choice of Hotel Agamemnon; not super-luxe but the BEST location... & early reserve gets you the BEST front room w balcony on the sea. You can easily spend 4 wonderful days with this as a "base," visiting Nemea, Mycenae, Asine, and going back via the coast road to see Epidaurus & make a brief stop at the Corinth Canal. Then you can finish with sightseeing in Athens.
•This fab Nafplio photo album https://www.flickr.com/photos/stanbr54/sets/72157632094108982/ is by RS contributor, stanbr: pix are in late Spring, but VisitNafplio website shows a video of Nafplio in winter and it's STILL wonderful. BTW, I consider Nafplio sunsets outdo Santorini's more-publicized ones ... and in Nafplio you can enjoy them even in November -- its seafront cafe's have Marquee tent-tops, with clear plastic windscreens and Heaters, so one can enjoy a sundown beverage in comfort.
PS: Santorini "luxury villa"?? Think twice! Villas will be isolated. In Nov, most activity, restaurants open ONLY in Fira Town.