It's going to be warm wherever you go, so I wouldn't worry about that, and Crete isn't significantly further south than Santorini (i.e., there's no difference in the weather). I think you can definitely see more of Santorini in two days than in Crete, but it's really your choice. Santorini is worth seeing for the caldera and now for Akrotiri, which has reopened. So you will get to see some ruins, though the ones on Crete are more spectacular.

If you really want the "beach" then Santorini isn't the best option and you might be better off in Crete. The beaches in Santorini simply aren't the main draw. Other islands have much better beaches.

If your itinerary on the mainland takes you near the coast (as it most likely will) there are many fine beaches there too, so you don't need to fly to Crete for beach time. You could get your sightseeing done in the morning & early afternoon, then head for a beach to cool off when it starts to get hot. Here is one example of a beach in the Peloponnese, and there are nicer ones than that: http://www.flickr.com/photos/heimdall_1/6171521331/in/set-72157627739427148.

With only two days to spare for the islands, my choice would be Santorini over Crete. If you are willing to pass up the spectacular scenery of Santorini and just want to spend some time on beaches, there are islands much closer to Athens that you could reach by ferry at a fraction the cost of a flight.

That sounds reasonable.

Would you consider Santorini your 1st choice of an island if you were only going to see one? We do not have to swim. We like to have a small amount of beach time on a trip.It does not have to be on the island portion of our trip.

We went to Spain last year and spent one day at the beach and it really a nice interlude on our trip

I think Santorini would be my choice if I could only see one island, but I go to Greece nearly every year, and don't have that decision to make. Book a room in Oia with caldera views, and the scenery will take your breath away. You can go to the other side of the island for a swim at the black sand beaches, or as brotherleelove suggests, down the steps from Oia to Amoudi for a swim off the rocks there.

One nice thing about Greece is you are seldom far from a beach, even in Athens.

Thanks for the info. I have to fight my cheap tendencies. I think we will go to Santorini. We will only be in Greece once, so we might as well see what we want.

Climate in the second half of September: Rhodes, Symi, Karpathos and Southern Crete are really warm and pleasant. In the Cycladic and North Aegean Islands, the weather may be fine, but it's no longer summer for sure.
I would fly directly after arrival at ATH airport to Rhodes or Crete, rent a car there and explore the Island (4 days for Rhodes, a week for Crete), give the car back and go by ferry to Santorini (the aproach by ferry is breathtaking, the flight is rather boring)and then by ferry to Athens.

I wonder if neckervd actually read the original post? James_P, you plan a week driving around the mainland, a few days on the islands, then finishing up in Athens. That sounds pretty good to me. Neckervd's itinerary is a completely different trip from the one you have planned.