Pamukkale to Kusadasi - Bus or train?

Bus. There is no train there. Take whichever company if any serves that. I don't think you will have too many choices.

Bus - if you haven't taken a long-distance bus in Turkey, they are very comfortable. The trip is about 3 hours, one change in Denizli.

Awesome - thank you.

Can anyone recommend a good bus company that they've used in the past?

Thanks!

There are several different companies. I always just showed up at the bus station, preferably in the morning, and took the next departure. The Lonely Planet guidebook should indicate the general frequency. More schedules might be online now, but the old way worked fine. You can also check schedules upon arrival if you're traveling by bus into Denizli and Pamukkale. You can sleep in Selcuk (also accessible by bus) instead of Kusadasi to be closer to Ephesus.

Pamukkale Turizm or Kamil Koc is the best ones I can recommend. Pamukkale Turizm has about 6 daily services.Pamukkale Turizm specialize in Turkish Mediterrenan and Aegan Coast services while Kamil Koc specialize in all Turkey but I would buy it from Pamukkale Turizm sure. Its 3.5 hours bus ride with probably Neoplan buses. They mostly use Neoplan buses.