4 week trip to Greece and Turkey

You don't say how much time you are devoting to Greece, so it's hard to suggest how many places you should see. Our trip was 15 days and included Crete, Naxos, and Athens. For a 2-week trip, I would suggest, at the most, only one more island in addition to your existing itinerary. Since you already have guidebooks (smart move), your best best would be to make a list of which locations have what sights and how assign a rating to each sight. Do you like beaches, archeological sites, nightlife, nature, etc.? Getting suggestions from other people is just going to add to the confusion.

I am going to be in Greece for about 2 weeks.

Before I went I did a google search for attractions or sights for every location I was considering.
Ask for "Athens sights" and do the same for every island or city you consider.
You will find detailed descriptions that will help you decide which place to see.
You can't use other people's decisions because our tastes differ so much. Your tastes will determine which places to see.

Hi Alison: Sounds like you could be a neighbor (we're in Napa Valley). Anyway, we were in Greece a couple years ago and plan to return next year. Definitely don't plan much time in unlovely Athens. The area we enjoyed most was Anafiotika, a little whitewashed village in the highest part of Plaka in Athens. A nice outdoor restaurant is Taverna tou Psara nearby. Mykonos is party central, but we enjoyed Santorini, particularly Amoudi Bay, where the tables of little cafes are so close to the water if you lean back too far, you'll be swimming. Forget the main touristy town of Fira. We rented an ATV and explored. Stay in the area of Imerovigli for fabulous crater views. There are many, many islands outside the Cyclades, which grab so much attention. We rented a house on the little island of Symi, which is lovely.

With two weeks, the secret is to look at a ferry route. It is a major hassle to visit two islands not on the same route, and it usually means a long wait at an island where routes cross, or going back to Athens. For Santorini, there are two sort of basic routes, the most popular hits Syros, Tinos, Mykonos, Paros, Naxos, Santorini. So any of those islands would be a good option. If you really want seclusion, you can take a ferry from Naxos and hit really small islands like Iraklia, Schinoussa, and Koufonissia, then back to the main route. Another major route is westerly of that one and hits Serifos, Sifnos, and Milos. Figure any stop will be at least 2 nights, if not 3; and to hit someplace like Koufonissia, probably 4. This is just due to the fact that most ferries run during the day, and will take up a good portion of that day.

As for other areas, not islands, Crete itself is more like a mainland than island, lots to see, and probably more opportunity for "non-touristy" stuff. The Peloponnese on the mainland is very nice as well. As for connection to Turkey, you could enter via Samos, otherwise, some connection through Istanbul.