RS Turkey tour ends in Ephesus: What then? Recommendations?

If you have a few extra days I would go back to Istanbul and stay there. Greece should be done as a separate trip as there is so much to see and do. I took the week long Istanbul tour and it was amazing. What a interesting and different city, where there was so much to see and do. You will not have that much time in Istanbul and it really is a great city to see in depth. We went from morning to night least amount of free time on any of the 12 tours I have taken and still we did not see it all. Plus ( I don't know you) but when will you get back to Istanbul to really see it. You will not be disappointed, or bored by the city. If you have any questions, pm me about the city. But I am sure whatever you decide it will be great.

When I was done I took the Best of Greece tour by RS and it was a great combination. If I didn't have enough time to do that, I would have stopped at Troy on the way back to Istanbul. A few more days there, possibly with a day trip, is always wonderful.

I would not add Greece unless you have at least a week for it, preferably more. Ferry connects you from Kusadasi to the closest island of Samos (port towns are Vathi and Pythagorio). From there, you can fly or take an overnight ferry to Athens, or take a fairly long ferry to another island chain, like the Cyclades; you usually go to a hub like Naxos then connect for other islands in the chain. You probably would appreciate a few extra days in Istanbul (fly from Izmir), especially if you you're shoppers.

I went by taxi with two others who went on to Rhodes by ferry. I spent the night in Bodrum, then did a seven day cruise of the Aegean with Barbbaros Cruises. There are several itineraries throughout the Aegean. There are also shorter cruises.

The Turkey tour spends little time in Istanbul. Even if you are arriving a day or two before the tour, you'll still have what to see for at least a couple of days after the tour.

If you have more time, then Greece by all means. A few of the folks on my tour had planned to take a ferry to somewhere in Greece on the way home, but it was already November and the ferries had stopped running for the season so they had to change their plans.

I do not know how many days you will stay in Turkey after your turn ends in Istanbul but if you look for closer places to Istanbul to visit, I would recommend Bursa city. Its old Ottaman Capital and you should visit Ipek Han (Silk Market) and Uludag there. Its 3 hours from Istanbul.
Second option I would recommend, go to Ayvalik in other side of Marmara Sea. See Ayvalik and they have daily ferry services from Ayvalik to Mytilini (Greek Island) .Its 25 euros round trip and 1.5 hour ferry ride from Turyolonline.