We stayed the night in Pamukkale. An hour in the waters should be enough. We spent most the time walking the ruins of Heiroplois. And on that day, I would estimate that less than 10% went to the ruins away from the travertines. Many more visited the ruins near the parking lots.

Thanx Dee_Dee!

That was my original plan. We will have a car so I guess we can decide then - and it will depend if we make it to Ephesus or not the day before.
I am interested in what I will think of Athens - I know a lot of people don't care for it outside of the big sites, but I am actually a city person so we shall see. I can't really cut a day off Athens as we are taking a direct flight from Athens and if we go the day before we will wont have any time in Athens.
Did you go to Aphrodisias as well? If so, how long did you spend there?

I've been in Kusadasi last year and taken a daily tour to Pamukkale from Kusadasi. If I chose going alone the cost would not be much different so I preferred an agency instead. They took me from my hotel in Kusadasi and we went on a daily Pamukkale tour. I must say the tour was organized properly and our tour guide was a really nice person. After the tour they brought me back to my hotel in Kusadasi. I guess they provide airport or bus station transfer from Denizli too. Here, take a look at their Pamukkale tour programs http://www.pamukkaletours.com/tag/pamukkale-tour/