Delos..To visit or not to visit // Athens then Santorini or Santorini then Athens?

Tough it out and go directly to Santorini. You'll be glad you did. Waking up that first quiet morning to the spectacular view of the caldera is something you'll never forget. Beats the hell out of traffic noise in Athens! Save Athens for the end of your trip so in case of any problems you have those extra days to get back to the mainland for your flight home.

If you are interested in history and the archaeological sites of Ancient Greece then you definitely should go to Delos.

Early October is still fairly busy, so there will be tourists wherever you go. And wherever cruise ships go you can bet it will be extra busy.

I agree with Lee. Going to Santorini on your arrival day doesn't waste a day at all. It makes very effective use of a day on which jet-lag will probably have left you at least semi-zombified. Now, figuring out the timing of that flight to Santorini is a whole 'nother thing. It is not safe to assume that your flight will arrive in Athens on time, so you'll need an adequate buffer before the scheduled departure of the Santorini flight. I've never had a first-day flight within Europe so don't really have an opinion about how much time you would need to allow.

What a great honeymoon! Loved Santorini and would have stayed at least 2 more days (we stayed 3 nights). If ruins are something you want to see, there are some very nice ancient ruins on Santorini https://www.santorini.com/archaeology/akrotiri.htm

We also went to Delos and loved it, but be warned that the seas could be rough and then it is not a happy boat ride. We actually went to Delos while on Mykonos. I really loved Mykonos because we stayed there, and were not one of the cruise crickets that hop off boat and then back on.
There is so much to Greece. I wanted to do more of the mainland this next fall, but found another trip.
Love love love Greece, the food and people.
If you are into food, I highly recommend culinary backstreets for a gastronomical tour of Athens. I did this and it was the highlight of my trip.
Congratulations and have a wonderful trip.

I see your problem. With a 10:30 arrival Athens the next flight to Santorini is at 11:40 which is too close to your arrival date to be sure to make the connection. If you flew with cabin baggage only you might have a chance but that really isn't much time.
The next flight unfortunately is at 3:50 so that means a 5 and a half hour wait. While I am a great believer in getting off to your first island immediately I can see why you would be "wasting " the day.
Athens is such a busy foreign city that can be overwhelming to first time jet lagged visitors which is why we recommend you get out to your island ASAP. I might suggest you keep watching the Aegean flights. Perhaps they may add an other flight after the new year.
If you book you hotels make sure you have free cancellation privileges. If a new flight is added perhaps you can switch your plans easily.
Santorini http://www.flickr.com/photos/stanbr54/sets/72157632154800782/
Delos is an amazing site but rather than taking the ferry to Mykonos, you might want to fly back to Athens and perhaps visit Delphi which is also an amazing site.
Olympia Delphi Meteora https://www.flickr.com/photos/stanbr54/sets/72157645469717811/
This will give you the opportunity to visit some of the Peloponnese after Santorini. Look at Nafplio it is a lovely sea side town probably the prettiest town in Greece. It will give you access to lots of day trips to ancient sites like Epidavros, Mycenae, Tiyrns, Ancient Corinth, Ancient Nemia and perhaps a long day trip to Sparti to see Mystras. Then head to Athens at the end of the trip. You will be used to how things are done in Greece and Athens won't seem so hectic.
Here are images
Nafplio and Peloponnese http://www.flickr.com/photos/stanbr54/sets/72157632094108982/

Trying to decide to stay in Athens on your arrival or continuing on to your final destination is a major questions on this and other forums. So much depends on arrival time in Athens and when the departure time is to your final destination, be it flight or ferry.

What we've done numerous times is arrive in Athens, stay for a day or two to catch our breath, see the sights and then fly/ferry to our final destination.

Since we have seen and done everything there is in Athens we always look for a way to bypass Athens. Health, age, physical fitness, time frame, stress level, not to mention flight delays play a factor on making a decision.

If you have more than two hours between your flight landing and your flight leaving you may be able to do it. More time would be better but that means hanging out in an airport for extra hours rather than getting to an accommodation in Athens and spending a day or two there.

This is always a tough call. However, Athens is really a great city, even though many consider it less than Paris, Rome, London, etc. we feel it's just right.

October is off-season and our favorite time for Greece, less tourists, lower prices and still nice weather. It's a great time to be in Greece!

We've did the Delos/Mykonis trip from Naxos and we loved Delos move than Mykonos. Delos is a World Heritage Site and is on par with Pompeii in Rome, not quite as well preserved but very similar. No one is allowed to live on the island and there are only a few buildings, one the museum and structures for archeologists and worker-related.

Mykonos, while visually stunning was too crowded, touristy and with 3 huge cruise ships in the bay spewing out hundreds of tourists made it not worth the time for us. But to each their own!

Thirteen nights gives you time to adequately visit Athens, Santorini and Mykonos. Although I've only read about Mykonos, it's my understanding it's more of a beachy island than Santorini - which I've visited including the Red Beach (pebbly) and Perissa Beach (volcanic). After landing in Athens, I'd head to Mykonos for a few days (including day trip to Delos), then ferry to Santorini and stay several days (we did 3 nights), then head back to Athens (fly - ferry is 8 hours) with several days in Athens to round out the trip.

Thank you everyone for your replies!

I think we are going to end up going straight to Santorini and hope that another flight is added that fits our time schedule a little bit better. Luckily we still have some time to watch flights before we need to book our rooms.

Thank you again!