possibility of long layover in Athens

I would definitely not plan a 1 hr. 15 min. connection in Athens, if that is what you're considering. Not unless you're very OK with not getting to Samos until the next day--and then only if there's a seat available on one of the next day's flights.

I'm not thrilled about the stateside (Philadelphia) connection, but that seems less risky than the alternative.

I don't quite understand your comment about American Airlines. Are there other flight options that are reasonably priced? What is your travel date?

have more than five hours in the airport, what can I do?

It's an hour taxi ride to get downtown, so considering you'd have to be back at least an hour early, and considering Athens traffic, you'd have to really be the adventurous type to try and go someplace else during those five hours.

That, however, should probably not lead you to making the overlay too short so you might risk missing your connecting flight.

“It sounds rather horrid”.....Actually I don’t find Athens a bad airport at which to wait for an onward flight.

Don’t forget, if Athens is your first stop in Europe you will be clearing immigration and picking up your baggage so allow an hour or more for that. Of course there is always the possibilty your incoming flight could be late.

The airport has lots of decent food outlets with fresh salads, pastries, and of course yogurt, etc on the main floor; they do tend to be busy, however. Otherwise there is a decent restaurant upstairs and a MACDonalds. Also upstairs is a small museum displaying artifacts found when the airport was built. I assume you are flying Aegean to Samos, you could look at using their lounge, or cross the road to the Sofitel Hotel and chill out there for a couple of hours.

I would rather a longer wait in Athens, and be sure of my onward flight than risk the short window of time for the flight from Madrid.

I wouldn't chance the short connection time with the Madrid flight. A delayed takeoff from Miami, delayed landing in Madrid, delayed takeoff from Madrid, delayed landing in Athens, maybe more than one of the above, and you're cooked. Unfortunately, the morning arrival wouldn't leave you much time for Athens itself given how long it takes to get back and forth from the airport.

The above-mentioned Sofitel has a comfortable lobby and café where you might even be able to take a little nap after your overnight flight. There's a nice little garden outside if you prefer to walk around in the sunshine. And you can practice your Greek reading the airport signs, with English translations supplied. Who knew that "Exit" in the Greek alphabet is pronounced "Exodus"?

Others are right that you are safer waiting for over 5 hours than waiting for 1:15, in case one flight leaves or arrives late. 2 or 3 hours would be an reasonable amount of time to wait in an airport, and this time you are sshhiht out of luck. Take the flight plan with the ovee 5 hour layover. Get some reading done, read or re-read a guidebook, walk around the airport once, eat at least once, watch airplanes take off and leave, and so on.