Itinerary Help...Crete or....?

I think Crete has everything you are looking for. Having said that Crete is very large. We have spent over 50 days there over the past few days and never got out of West Crete.
Naxos in many ways is like Crete but smaller. It too has everything you are looking for and logistics from Santorini to Naxos work very well.
I would do 3 nights Santorini for 3 nights then Naxos for 6 then back to Athens at least one day before your return flight. Here is what Naxos is like there are lots of beaches and hikes.
Naxos Mountains and Villages http://www.flickr.com/photos/stanbr54/sets/72157632110674306/
Naxos Town http://www.flickr.com/photos/stanbr54/sets/72157632094558042/
Trip around Naxos http://www.flickr.com/photos/stanbr54/sets/72157634605629689/

Thanks Stan! You mentioned we should look at Naxos for 6 nights. Am I overly ambitious to think we could do Naxos for 3 nights and Paros for 3 nights?

This would be our itinerary:

9/4 Arrive in Athens-Fly directly to Santorini for 3 nights
9/7 Take a Ferry to Naxos for 4 nights
9/11 Take a Ferry to Paros for 3 nights
9/14 Take a ferry/flight to Athens for 2 nights
9/16 Depart

Your revised plan for both Paros and Naxos works fine. I think Naxos deserves a week just to get to know your way around. Since you are traveling in September the hotels won't be full. Why not get to Naxos and at the end of 4 days decide if you want to stay. If so you can easily find another hotel and extend your stay. If you feel you have had enough of Naxos just hop the ferry to Paros and look for a Hotel there. There will be hotel owners meeting the the ferrys so you will have your choice of hotels. This time of year gives you lots of flexibility.
One good idea for this option is to do some research on where you want to stay. That way you can ignore the hotel people located someplace else.

I like the idea of 3 islands, but for a completely different experience -- instead of Paros I would recommend a small island, either Amorgos or Antiparos.

There are daily ferries between Naxos & Amorgos. On Amorgos, stay in the main port of Katapola. So scenic and inexpensive. Great place to wander. It has the famous Hozoviotissa monastery carved into the side of a cliff.

Or ferry from Naxos to Paros and then take a little ferry to Antiparos. Here you'll find a famous cave with stalagmites & stalactites. And here you can take a great all-day boat trip around the island --"Lazy day with Captain Ben". A highlight of our recent trip.

Antiparos might be easier logistically as there are ferries back to Paros & lots of ferries to Piraeus (Athens port). Also AEGEAN airlines has recently started flying to Paros so you might grab a cheap flight.

I agree that Amorgos would be an exceptional island to visit, still not overly touristy, lovely villages in the mountains, fantastic monestary on a cliff side, beautiful Chora, Katapola would be my choice of towns to stay in. We were there in mid-October for 6 days and it was just beautiful . . . and not many tourists!

I understand wanting to see as many islands as possible but sometimes it's better to slow down and appreciate where you are and letting the experience soak in rather than rushing from island to island.

But to each there own . . . regardless you'll have a great time!