Not us, but in 2010 we flew from Istanbul to Izmir then by train Izmir to Selcuk and three nights at tripadvisor favorite Hotel Bella.
(One caution for Hotel Bella--stay away from the rug store in the lobby, and if you're looking at rugs elsewhere make sure the owner doesn't know about it.)
Saw Ephesus on our own and took full day bus tour PMD the following day to see Priene-Miletos-Didyma.
Didn't have another day so we missed seeing Pergamon.