Had a great time in Athens staying at Yagos place. It's small but has a beautiful terrace and we especially liked the neighborhood. It's right by the museum and close to a large park for jogging. The metro is close as are the buses to other towns such as Marathon. It doesn't seem touristy at all and we felt like locals.
Yagos recommended a Cretian restaurant that was wonderful. It's hard to find but worth the effort. By a bottle of the Crete national drink and share it, you'll make lots of friends.