Does it make any difference if we fly back to Athens from Naxos or Paros? I looked at he Aegean Air site and it doesn't look like they fly from either Island. Is that correct? thanks

The difference is that only Olympic Airlines flies to Paros and Naxos, and they have a terrible reliability reputation, not to mention the fact that they're more expensive.

If you're on Paros you can get back to Athens by car ferry or by first taking another ferry to Mykonos and then a highspeed ferry to Rafina and a bus into Athens.

hmmm-would it make sense to go by ferry from Crete to Naxos or Paros and then go to Santorini where we can fly Aegean back to Athens?

If you do you'll have to backtrack, but I don't see how you can avoid it if you want to see Santorini last. The ferries from Crete stop at Santorini first. The highspeed ferry from Heraklion goes to Santorini-Ios-Naxos-Paros-Mykonos.

http://www.greekislands.gr/hfd/

There is no reason to complicate things. Paros and Naxos have frequent ferries back to Piraeus, in the summer there is also hi-speed catamarans almost as quick as flying.

This would be in the end of September on our return to Athens to fly home the following day. I've been reading about the ferries not being able to go given the weather. Thus the reason for wanting to fly back to Athens. Does anyone know if September is one of those months that has a high likelihood of ferries being unable to go? I know its not possible to predict, just wondering what past experience has shown.