I agree with the suggestion to not go to the small islands. Actually, it's maybe best not to go to any islands at all, since Crete and Rhodes and Corfu do have large local populations, but they (at least Rhodes and Corfu; maybe Southern Crete is better) are incredibly wet and rainy during winter.

I suggest you look into the following places:

Thessaloniki- SKG(the country's only major city apart from ATH): interesting churches, fabulous food, Macedonian remnants in the vicinity (you need to rent a car for these), decent scenery by the sea (don't expect to swim).

Ioannina - IOA- and Metsovo: it's going to be freezing there, but they're a bit of a timewarp...traditional architecture, hiking paths, a lake in the middle of the city, a seriously slow pace of life, and again some food to die for.

"Alternative" destinations:

Kavala - KVA: mid-sized city with good scenery, and near a major ski centre

Nafplio (not far from ATH): similar to KVA, plus it's got an ancient theatre nearby, as well as some more archaeological stuff in nearby Korinthos (Corinth).

If you must go to an island, CFU is the most beautiful. But it WILL be rainy.

Aegean (A3) have plenty of flights to all of the above places. Good train service to SKG, mediocre to KVA.

Hotel in Athens: that's a tough one. Classical hotels are running some pretty neat prepaid offers at the moment. EUR89 per night for a superior room in the 5-star Acropol! ^