What time of year are you going? If it's a warm-weather month, I'd see Ephesus first thing in the morning. Afternoons can get very hot and more crowded.
As for antiquities, of those on your list we have only seen Pergamum. It's an interesting site, with the best-preserved amphitheater we've ever seen. But I don't know if it's worth the time/effort on this trip to go there, as the site is not nearly as spectacular as Ephesus.
We visited Turkey's Mediterranean coast three years ago. I wrote a trip report, which I'll link here to save me rewriting everything. We didn't visit Bodrum, so I can't really comment. We did visit Fethiye one day and I didn't find it especially appealing. We were in Marmaris just overnight, to catch the ferry to Rhodes, and that was plenty of time for us.
Regarding ferries: the availability of ferries from Bodrum and/or Fethiye to Rhodes depends on time of year and sometimes, weather. There is a dependable ferry from Marmaris to Rhodes every day (and when I was researching, it ran twice a day, in summer). So we chose to depart from Marmaris.
That leaves the question of where to stay along the Turkish coast for a few days. I could recommend:
1) The tiny, tiny town of Patara, with its huge, sandy beach. We stayed in the wonderful, inexpensive Akay Pension where they served the best food we had in Turkey! And Patara has some ruins, too, outside of town, which you walk (or drive) through on your way to the beach. Your girls might enjoy the nearby Saklikent Gorge. And I think Xanthos is near Patara, but we didn't go there. We did a day trip (boat) to the nearby sunken city of Kekova, which was fun. Patara is about 2 hours south of Marmaris.
2) Dalyan, which is more developed than Patara; its main attractions are Lycian tombs carved into the hillsides along the river that runs through town, and a sea turtle rehabilitation center, which we found fascinating. You can take a river boat to see the tombs and have a mud bath (interesting!). More tourists here, so more restaurants and shops, but not over-run. I don't think you'd find package tourists here (they're all in Marmaris!). Dalyan is about 1 hour south of Marmaris.
We also stayed in Datca, a little town just across the bay from Bodrum. Extremely small and quiet. Main attraction were the ruins at Knidos, which we really weren't impressed with. It's a huge site with very little restoration, and it was miserably hot the day we were there. I wouldn't recommend Datca for you.
As for the buses, that's all we used and they worked great for us. But you might want to consider renting a car when you leave Selcuk and dropping it off in Marmaris. Driving in Turkey looked pretty easy.
