Greece and Turkey Sept 2018

I was hoping that someone with more recent experience would have replied to your post by now.
Our infö on Greece is from 2007 and Turkey 2010. We spent a month in both countries and am sure you will love both.

Regarding Greece, we visited Mykonos, Santorini, Lesvos and Crete. Can't help you with the other islands. I think your idea of spending 2 days per island "so that we can really soak up the islands" is not realistic considering transit and checking in times. I would select 2 islands.
We liked Mykonos its a quirky little town high on partying. We visited a couple of beaches and found them small. The highlite was the trip to Delos. You can spend several hours there exploring this specular site.
On Lesvos we stayed in a small fishing village on the north of the island called Molyvos for a few days and then moved to Mytilene for a couple of days. We would recommend Molyvos.

For Turkey you mention renting a car, visiting a few places and making your way to Istanbul. It isn't clear if you are planning to drive to Istanbul and drop off the car before going to Cappadocia. From the research I did, there is not much to see at Troy. We were in all of the other places you mentioned and really enjoyed them. Selchuk is the major town serving Ephesus.

If it were me I would skip Troy, visit the other areas and drop off the car at Izmir airport which is what we did. You can get a flight from Izmir to Kayseri (Cappadocia) via Istanbul (there don't seem to any direct flights from Izmir to Kayseri. In Cappadocia we rented a car and stayed in Goreme for 3 nights in a cave hotel.

I hope this helps. I can research our notes and answer more specific questions if you have any.

Greece: Naxos, Delos, Mykonos, Samos, Lesbos. Let's see how that works. From the Athens airport you can fly to Naxos (but you're taking a chance buying separate tickets since you could miss your flight and be out of pocket. Or you can take a taxi to Piraeus and the a ferry. Depends on whether you have to pre-book the ferry and what the schedules are for ferries and flights. Early September is probably high season. Okay, you spend 3N on Naxos (1 day in Naxos, 1 day trip to Delos. Then on the 7th, a ferry to Mykonos 2N (1 full and 1 3/4 day there). On the 9th, a 5 hour ferry to Samos for 2N, so one full day plus a bit there, and on the 11th you're leaving for a long journey to Lesbos (Mytilene) - 5-6 hours by ferry (BTW I'm using rome2rio.com to find transportation). If you stay 2N, then you leave for Turkey on the 13th. That's another 1/2 day with ferry, passport control and car rental. That's a lot of moving around and it doesn't look like ferries run every hour or so. Will you have enough time to see the sights you want to see in each place? If you just want to "soak up" the sea, sun, beaches and tavernas, I'd really expect them all to be much the same and you are likely to have a better trip if you stay in two places and have the time to enjoy them. What I'm trying to say is that 2N is not the same as 2 days. If you want 2 enjoyable days, you need 3 nights. That's even more true for Cappadocia.

In early September, I would expect it to be necessary to book rooms in advance (maybe even now is not too early) and also to get ferry schedules. There are various companies and more than one type of ferry. While there are probably multiple ferries for short trips (like Naxos/Delos), there may only be one or two ferries a day for longer trips - or perhaps not even daily.

I haven’t checked ferry schedules for October, but based on previous years, you may have problems ferrying into Lesvos from other islands in September. The easiest way to get there is the 1-hour flight from Athens.

My suggestion — based on several trips to Lesvos and to Turkey — is that you consider restructuring your trip. Save the Greek island hopping for another trip. On this one, fly directly from Athens to Mytilene (Lesvos). Go directly to Hotel Votsala via taxi and spend a few days there. It’s a wonderful, inexpensive place right on the sea, where you can walk down the beach to a taverna for fresh fish. The owner, Iannis, a charming amateur archeologist who takes guests on optional excursions. The kindest, most hospitable man we have ever met. The hotel is filled with repeat guests. Mostly European. We’ve been there 5 times. After a few days, rent a car (it will be delivered right to the hotel) and circle the island. It’s the 3rd largest Greek island with lots to see. You might spend a night at Molyvos, a charming seaport, and visit the nearby thermal springs. Drive to Sigri, and then on to Skala Eressos, a gorgeous beach. Further south is Vatara Beach, miles of white sand. Drive to Plomari and tour the ouzo factory. Spend four or five nights touring the island, then return your car in Mytilene and ferry to Turkey.

Your plans there sound good. Bergama (Pergamum) is a really evocative site. And the amphitheater is amazing. Be sure to visit the nearby Aesclepion, a 4th century BC medical center. It might be worthwhile to have a guide here as well as for Ephesus.

Be sure to take a hot air balloon ride in Cappadocia.

Another thought — If you decide to cut Greece to just a week in Lesvos and have more time in Turkey, you could drive down to Bodrum, which is beautiful, and then further south along the coast to Dalyan. This is a pretty little town, very popular with the Brits, where you can take a river cruise to see the Lycian tombs carved into the cliffs, and end up with a mud bath. Quite the experience. Dalyan also has a interesting sea turtle hospital. You could then drive to Cappadocia, then to Istanbul (or perhaps drop your car in Cappadocia & fly back to Istanbul. Then you’d have all your Istanbul time together at the end.

Lots of options!