I went on a tour in 2010 along the west coast of Turkey, zigzaging to Greek Islands. These are the sites we visited in Turkey that I would recommend:
Bergama - the ruins of ancient Pergamum. There is a lot here including an Asclepion, the acropolis of the town with remains of a hillside theatre and temples (we didn't get to explore here much because we got there in the middle of a thunderstorm but I really would have liked to have seen more).
Ephesus - a must see of course. Hopefully there won't be three cruise ships worth of people visiting when you go like there was the morning I was there. Pay the extra money and go into the House of the Slopes if you like mosaics.
Between Kusadasi and Bodrum - Miletus, Priene and Didyma. I enjoyed all three and they were very different from each other. Lots to see.
If you don't mind taking a ferry over to Kos from Bodrum, it is worth a day trip at least. There is the huge Asclepion, a Roman town, a Greek agora, an Odeion and the Plane Tree of Hippocrates.