I can't imagine choosing a hotel over a neighborhood apartment. This is a pretty typical Athenian apartment with big French doors to little balconies off the livingroom and bedrooms. Some North Americans might have trouble adjusting to the quirks of Mediterranean plumbing (e.g., having to heat water for showers), but if you're looking to experience another country and not just to see it, then you'll appreciate the quirks.
The metro is a few minutes walk down the hill, as are trolleys and buses, so you can still get to museums and historical sites, but you also get to experience a real (residential) neighborhood. If you want to prepare your own food, you certainly can (we have), as there are plenty of pots, pans, dishes, and utensils, and there are two supermarkets just down the street, not to mention smaller shops. If you don't want to cook, there are also plenty of restaurants, cafes, and bakery/patisseries within a few blocks.
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