Pamukkale, cappadocia, then istanbul

A Lonely Planet Turkey book is a must...it will tell you your options for getting to those places, and it's a great resource for Turkey in general. You can either fly or take a bus to Pamukkale and Cappadoccia using Istanbul as the base. It's very likely that you won't be able to avoid beginning in Istanbul AND ending in Istanbul because Turkish Air flies there. Perhaps flying into Ankara and out of Istanbul would be better, but check with Lonely Planet.

Lonely Planet guides are very good for Turkey. The long-distance buses are very comfortable (you will probably be offered water or tea, a splash of lemon cologne, and maybe a cookie).

If you land in Istanbul, you could go to either Pamukkale or Cappadocia first.

I am almost reluctant to mention it, but no Ephesus?

I know I know but we have only about 6 days and I don't want to miss anything in these cities by squishing in more places. :/

Can you provide some more information on your travel? Will you already be in Pamukkale? If not you'll probably be flying through Istanbul and on to Denizli. From there you'll have about a one hour drive to Pamukkale. If you're driving from Istanbul it will take you about eight hours. From Pamukkale it will be another eight hour drive to Cappadocia or a flight to Kayseri and a drive to Goreme. You'll have a similar flight or 8ish hour drive back to Istanbul from Cappadocia.

Unless you have a real interest in geology with six days you might want to consider dropping Pamukkale. In my opinion it is the weaker of the three locations on your itinerary. Another option is to drop Istanbul except for maybe a brief taste and save it for a future trip. A decent visit to Istanbul takes about four days and the top sites in Cappadocia can be done in two days. Pamukkale and adjacent sites can be seen in one full day. Because of the travel time factor I don't think you can see all three.

You should consider renting a car in Cappadocia. The sights are spread out and not well served by local transportation (i.e. without a car you'll need to sign up for a tour or hire a guide). A car will also let you visit top notch sites that are not served by tours.

Have fun!

We are spending a total of 2 weeks on our trip, half in Greece and half in Turkey. I found a flight from Athens to Pammukale for cheap, but I haven't made any decisions yet about that. The only plans set in stone at the moment is that we are starting our trip in Athens and we need to end up in Istanbul for our flight back to the States. Everything else is up in the air although we just want to see as much of Turkey as we can.
-Ciara

We have even thought about doing Cyprus in between Greece and Turkey, but we really want to see Cappadocia and I couldn't find any practical ways to get from Cyprus to Cappadocia. In that situation we would be only doing Cappadocia and Istanbul in Turkey.
-Ciara

I don't know enough about flying between Greece and Turkey via Cyprus, but given the political situation/divided territory it does not surprise me that there are no flights that allow for this.

I certainly understand not wanting to miss Cappadocia. The west coast of Turkey and Istanbul would be easier to see in your case, but I think Cappadocia is a more unique place to visit. Although I think it would be more restful to see just Cappadocia and Istanbul, your schedule is possible in six days if you fly early/late and rent cars. You will use about 1.5 of your 6 days for travel.

Unless you found a direct flight from Athens direct to Denizli, you'll have to come through Istanbul to get to Pamukkale. From Athens I’m guessing that it will take about 4 to 5 hours (two short hops with a short layover in between) plus another 20 minutes of driving. You’ll probably also have to come back through Istanbul to get Kayseri or Nevsehir (the two closest airports for the sites in Cappadocia). Figure another 4 hours for two flight segments/layover plus a 25 to 50 minute drive. Nevsehir is closer to Goreme which has more hotel and restaurant options than some of the other towns in the area. The flight back to Istanbul would take about 1.5 hours of flight time plus travel time into the city. Add in a bit more to the travel time if you’re planning to check bags.

Under than plan your trip would look something like this:

Day 1 = Flights to Pamukkale, ½ day in Pamukkale.
Day 2 = ½ day in Pamukkale, Flights to Cappadocia
Day 3 = Cappadocia
Day 4 = ½ day in Cappadocia, Flight to Istanbul
Days 5 and 6 = Istanbul

Given the time contraints above, I'd spend my time like this:
1. In Pamukkale divide your time between the travertine, pool, Hieropolis and the museum.
2. In Cappadocia see Goreme Museum/Buckle Church and nearby fairy chimnies, Uchisar castle, Kamakli underground city, and Sarihan caravansary/Avanos village. If you have extra time add on the Church of St. John in Gulsehir, Eski Gumusler monastery in Nigde or the Devrent Valley.

3. In Istanbul see the Topkopi Palace, Aya Sophia, Hippodrome, and Blue Mosque. This will take one very full day. Use a guide book based on your interests to fill out the second day.

We have even thought about doing Cyprus in between Greece and Turkey, but we really want to see Cappadocia and I couldn't find any practical ways to get from Cyprus to Cappadocia. In that situation we would be only doing Cappadocia and Istanbul in Turkey.
-Ciara

Ciara, I will give you a practical way to go to Cappadocia from Cyprus by assuming you will be in Greek side
You cross into Turkish side and take a flight from Ercan Airport to Antalya via Pegasus Airlines. Pegasus flies daily between Turkish Cyprus and Antalya. Once you arrive to Antalya ,you can fly to Nevsehir Airport with Anadolu Jet which is subsidary of Turkish Airlines. They fly 5 times weekly between Antalya and Nevsehir. This is new flight service starting in the end of April.
You can try Kayseri Airport too. Kayseri Airport is bigger than Nevsehir airport and there are more daily flights to Kayseri. Kayseri is 45 min drive to Cappadocia too but I am not sure if there is flight between Kayseri and Antalya.