Early July trip to Greece for 16 days

I like the idea of getting to one of your island destinations upon arrival in Greece, but I really think you're trying to squeeze too many different destinations into the pre-Athens part of your trip. Before you get comfortably relaxed anywhere, you're going to have to head to the airport or ferry port. It is really dangerous to list the same day in two different places as you are doing. It tends to give you a false impression of how much usable time you'll have in each place. In truth, most of any hotel-change day will be lost to travel time, so such days aren't worth very much in either the departure or arrival city. This is how I'd record your plans:

Day 1: Arrive late in Crete (3 nights). (What city?)
Day 4: Ferry to Santorini (2 nights)
Day 6: Ferry to Milos (3 nights)
Day 9: Ferry to Athens (6 nights)
Day 15: Fly back home

The number of real, full days you have at each stop is one less than the number of nights (Crete 2, Santorini 1, Milos 2, Athens 5).

Some specific comments:

• Especially with a really late arrival on Day 1, you may still be dragging on what I'm calling Day 2 (which you were counting as Day 3). Crete is huge, it takes quite a long time, in some cases, to move from point to point. The key sightseeing attractions are in the west; the party-hearty spots are in the east. A huge island is not a great choice for such a short visit. And once you're in Crete, you have quite a long ferry trip to the Cyclades. Although Crete is my favorite of the islands I've seen (which is only 7), I wouldn't go there for just 3 nights. That's only 2 days, and one of those may be somewhat jetlagged.

• Santorini is expensive and very touristy as well as very scenic. I think quite a lot of people probably only spend two nights there.

• I haven't been to Milos, but I imagine it will be a nice contrast to Santorini.

• Athens has some incredible classical sites and museums. Except for the (very touristy but ancient) Plaka, it is not a very attractive city, to my mind. It doesn't have the large neighborhoods of gorgeous historical buildings you'll find in most other European capitals. I think five nights is a very long time to stay there for the vast majority of tourists.

I'm not sure what's going to happen, price-wise, when you try to buy a one-way ticket to Crete. This has just occurred to me: Do you live in Europe?

Thank you so much for the response. I would be flying from the US so that would be where I am coming from/leaving. Would it be better to fly into Athens and then fly down to Santorini and pick another island that is closer to Athens? Or would you recommend more time on Crete since you are saying it is so nice.
Idea 1:
Day 3 Crete (5 days) we would rent a car and drive around the island. Any area you would recommend to stay?
Day 8 Santorini (2 days)
Day 10Milos (3 days)
Day 13 Athens (3 days)

Or
Fly into Athens instead then fly to Santorini
Day 3 Santorini (2 days)
Day 5 Milos (3 days)
Day 8 Mykonos (3 days)
Day 11 Athens and day trips around the mainland (5 days)

Sara you are still missing the main point and are trying to cram way too much into a very short period of time. Greece is a place that should be enjoyed slowly so you can absorb the culture.
As noted every island hop eats up a half day so you are spending a third of your time jet getting around. Minimize the island choices will allow you to maximize your experience.

If I were to choose two islands I would fly to Santorini on arrival in Athens. Santorini is great for about 3 days but then the high prices and the cruise ship crowds become hard to take so its time to leave.

Ferry to Milos and enjoy your time there. Fly back to Athens. Athens does require some time to visit all the main sites but three days will be enough. By cutting your Athens time you now have extra time to add to Santorini or Milos. Milos by the way certainty deserves a week.

Alternatively you can go to Crete instead of Milos. While Crete is huge and needs a month to do it any justice if you concentrate either the east or the west you do have sufficient time to enjoy that one area.

Maybe this will help.
Santorini http://www.flickr.com/photos/stanbr54/sets/72157632154800782/
Western Crete http://www.flickr.com/photos/stanbr54/sets/72157632115757899/
Chania http://www.flickr.com/photos/stanbr54/sets/72157632117917828/
Milos http://www.flickr.com/photos/stanbr54/sets/72157632109429236/
Milos http://www.flickr.com/photos/stanbr54/sets/72157634779985764/

We were in Greece for 14 nights and went to four places. We spent 3 nights in santorini (flew to upon arriving) ferried to Naxos for 4 night, then flew to Athens and rented a car. We then spent 4 nights in Nafplio and returned to Athens airport and spent 3 nights in Athens.

I do not personally think 4 locations for two weeks was too much moving around, although I would have loved 5 nights in Naxos and 4 in Athens. But two nights in any of the islands is a lot of trouble for very little gain. It took us more than half of a day to move from santorini to Naxos. We left where we stayed first thing in the morning and were not ready to do anything until around 3 pm.
So if you were to only stay 2 nights you basically would spend as much time moving as on the island. You would only have one day on the island and be traveling for one day. That is what is hard to understand until you have done it.

That pace is not good for the independent traveler.

Crete is wonderful - but large - and probably deserves the better part of a week just to see part of it. You do Crete and then fly to Athens and just do those two. OR - Start in Santorini and add in a couple more islands on the way to Athens. The most popular route would include Naxos/Paros/Mykonos (pick two). But I recently did Santorini-Fologandros-Milos- Sifnos (then you'd go to Athens after that). Even though you are still changing hotels every few nights, at least those islands are small and they are all on the same route.

Here's my trip report from that trip - might give you an idea of how long each island 'warrants'.
https://andiamo.zenfolio.com/blog/2018/11/greek-island-hopping-santorini-folegandros-milos-sifnos
https://andiamo.zenfolio.com/blog/2018/11/greek-island-hopping-2018-part-2-milos-sifnos-and-folegandros

On that same site are my photos of Crete and of the mainland/Athens

I would seek out places other than Athens for your last 7 days. As many times as I've been to Greece I have never felt after two days in Athens that I needed more time there. Yes, there is enough to do with more time but after you've been to those other places being in a steaming hot crowded and noisy city like Athens will be a letdown.

Consider renting a car at the airport and driving out to either Nafplio, Delphi, Meteora, Monemvasia, Olympia (among the hundreds of choices) instead of the extra days in Athens.

We spent about a month in Greece 2 years ago. We arrived in Athens 2 days prior to the RS Greece Tour. We felt we had a great Greece experience (see tour itinerary). Following the tour we went to Santorini for 4 nights and Naxos for 6 nights. We felt that 3 nights in Santorini would have been plenty.

We preferred Naxos for the beaches and unpretentious experience. We were fortunate to get excellent advise from the contributors on this Forum. With limited time I think "less is more." I agree, less time in Athens and expand your time in Nafplio and surrounding area.