I have used packing cubes to hold all one type of clothes like all my shirts. The idea of putting outfits in them is a good one.
We plan to drive to Delphi and Meteora because as noted the public transportation isn't very flexible. The public transportation we are considering is to the south west coast of Crete returning to Chania to rent a car for remainder of our time there. The buses actually run early and late there.
We have 2 or 3 one night stays planned. I say 2 or 3 because I am considering consolidating one of them. I wonder what others think--seems like many have been to Crete. I have us staying in Zaros after exploring the Amari Valley but could drive another hour to Archanes where we already are staying 2 nights so make it 3 nights in Archanes. Overall, I calculated it would mean 90 minutes more driving than staying in Zaros as we would have to backtrack to go to Gortys the next morning.
And Jessica--we did visit Greece with 3-4 night stays and loved it. I think it depends where you are going. We went to Santorini, Naxos, Nafplio, and Athens--all of which lended themselves to staying put. Crete is too large with sites spread out for that approach I am finding out.