Athens to Crete - 11 days
 

My husband and I are planning a trip in Sept. to Greece. Our plan is to start in Athens and travel to Mykonos, Naxos, Paros, Santorini, Crete and then back to Athens to fly home, we have 11 days. Should we do Athens at the begining of our trip or on the back end? Is 5 islands doable for our time period? We are open to staying on one island and doing day trips if that helps with time. Suggestions please...

I don't see how you can begin to visit all of those places in only 11 days. Perhaps Athens, Paros Santorini..or Naxos in place of Paros. Or Athens Mykonos, Paros(or Naxos) Santorini, or Athens, Crete perhaps with a stop off iin Santorini. Crete is very large and you could spend the whole eleven days there.
The ferry from Mykonos goes to Paros. Paros is very near Naxos.
You can fly to the first island and then ferry between them, flying back to Athens from the last island.
What time of year are you thinking of traveling to Greece?

It's possible to travel between all those places in 11 days, but not to see them as well!
To help with the paring down to a reasonable itinerary what are your interests/preferences once you are there? Scenery, beaches, history, walking? What made you pick these islands in particular?
Leave Athens until last, it means you are within easy reach of the airport for making your homeward flight, rather than having to make a connection from an island.
The only way to fit in as much as possible of your list is to fly straight to Santorini on arrival for a couple of days, then ferry to either Naxos or Paros for 6? days, you can visit one from the other, as well as a short visit Mykonos(& Delos), then fly if possible (time factor) back to Athens for your final 3 nights.
Crete is not worth including unless you forfeit most of the rest of your itinerary, it's too big to just visit for 1 or 2 nights.

I'm planning a trip for September as well - after reading the many posts on Greece, I planned a 16 night trip, as follows:
Crete (6 nights), Santorini (3 nights), Naxos (4 night), Delphi (1 night), Athens (2 nights).

I completely agree with the others that seeing 5 islands in that time frame is unrealistic, and you're much better off whittling it down to 2-3 islands.

I don't know your interests, but I agree that Crete most likely should be eliminated. It's a large island and unless you want a "drive-by" experience, it's probably not worth the time/cost to get there for 1-2 nights. But try to figure out what your priorities are for seeing and then revise the plan.

Assuming that your total trip is 11 nights, you should probably plan on at least 2 nights in Athens at the end. If you fly to your first island right after you arrive, you'll be able to maximize your time.

You could conceivably fly to Crete (4 nights), then ferry to Santorini (2 nights), and ferry to Naxos or Paros (3 nights); or skip Crete, and go directly to Santorini, then go to 2 of the other 3 islands (Naxos, Paros, Mykonos).

So once you decide what it is you're most interested in, it will be easier to figure out what the priorities are.

The islands may look close together on a map, but each transfer eats up the best part of a day. Ferries don't always leave an island when most convenient for you, and move at about 30 mph, so progress is slow. With your proposed itinerary you will spend every other day checking out of hotels, transferring to ferry ports, waiting to board ferries, travelling to the next island, and checking into new hotels. Half of your trip will be wasted in travel between islands, with little to see from the ferry.

Even three islands and Athens are too many. Recommend picking at most two islands on the same ferry route, e.g. Santorini and Paros or Naxos, and save Athens for the end. As yiassas mentioned, flying direct to Santorini upon arrival in Athens will save time. :-)