Question about Turkey and Greece Travel by car or bus

Thanks for all your suggestions. I am feeling more confident about Greece and Turkey. My tentative plan is 2 weeks in Greece and 3 weeks in Turkey. And I think a car most of the time with a bus here and there and a flight or 2 in Turkey sounds the way to go. Thank you also for pointing out how to avoid backtracking.
As for Greece, we will most likely go with a car in the Peloponese area.

You can fly from Izmir to Kayseri to see Cappadocia. Pegasus Airlines has direct flights. From there it is a cheap shuttle service to your hotel in whatever town you choose to stay in. Flight was very cheap when bought in advance.

Thanks Kate for the information. I was having problems with buses from Bodrum to Cappadocia. So I guess it has to be Cappadocia after Ephesus, if we decide to go by air. I will have to see how to get to Bodrum from Cappadocia. I did come across one posting on another question. This person said driving from Izmir/Selcuk to Bodrum took only 3 hours and that that particular area was fine for driving.
Looks like Turkey transportation will have to be air, train, bus and car. Quite a mishmash.

We would recommend driving. We just returned from 4 weeks in Greece and spent 13 days driving through the Peloponnese. We left the rental car at the Athens airport and took the metro into Athens to avoid driving in Athens. Last year we spent 21 days in Turkey and also drove there. The roads are excellent - we found them to be much better than our roads in California. There was little traffic.
In Turkey, after spending time in Istanbul we flew to Cappadocia and rented a car there for 3 days so we could visit the sites at our leisure. We took the overnight bus to the city of Antalya and rented another car there for 8 days driving along the Turquoise coast to Selcuk and leaving the car at the Izmir airport to fly back to Istanbul. If you go to Selcuk first and have time for Cappadocia (which we highly recommend) you could either fly or take the bus as it is quite a distance. In Greece, we visited some islands then picked up our rental car in Pireaus. We visited the sights you mentioned plus a few more in our 13 days making a loop ending in Athens. Some of the roads were windy but all were well maintained and well signed. We had no problem driving in either country. We have also driven in France and Portugal and would say that the conditions in Turkey and Greece are similar. We felt that driving allowed us to be more in control of our schedule and freed up more time to spend at the sites.

Forgot to mention that you can also fly to Cappadocia from Antalya airport. If you can find a bus from Bodrum to Antalya that might be a solution. Going from Selcuk to Cappadocia and backtracking to Bodrum seems to be a lot of backtracking.

Two websites that were invaluable for my (very different from yours) Turkey trip: http://www.turkeytravelplanner.com/ for all kinds of information. He has detailed sections about getting around by bus, train, car, and plane. He also has lots of details about each place in the country, like what airports serve what places (yes, Bodrum and Cappadocia can be reached easily by plane, although you may have to connect in Istanbul or Ankara depending on the specifics of where you are coming from). http://www.bulucak.com/ for finding flights within Turkey. This like Kayak, but just for Turkey; it searches all the domestic airlines, and you then go to the airline's website to book directly. When I used it last year, the English option was working. It no longer seems to, but it follows the same format as other similar sites (departure city, arrival city, one way or round trip, and dates of travel; use a translator for the months, to be sure). Turkish airfares are cheap in advance, but go up closer to travel. Flying within Turkey is quite pleasant; the airports (at least the ones I saw) are modern, the flights are short, and despite the shortness, you get a beverage and a choice of sandwich or cake (yes, included in your ticket price, not for an extra charge).

Thanks ever so much, Harold. I already knew about the Turkey travel planner but I was not aware of the air travel website. I am also looking at some sample itineraries and then changing them to match our needs. I am quite familiar with Italy, have been there several times. But many of my friends have been raving about Greece and especially Turkey. And I am realizing why. There is so much to do and see in Turkey that we may have to leave some things for the future, just like we did with Italy!
Thank you once again to all of you for your help.