When we took the Jordan extension, they flew us on Royal Jordanian. As good if not better than the EgyptAir short hops.
Despite the pride the Egyptians and Jordanians have in their peaceful relations with Israel, our flights did not fly over Israeli air space. Therefore the 2 hour flight time was correct.
The toughest part of the trip was getting home from Jordan. We didn't investigate a direct flight from Amman to New York. With benefit of hindsight, it probably would have been the better choice.
We were routed back through Cairo at the end of our Jordan extension. The lines were looooong. Egyptian citizens get priority. A group from Overseas Adventure Tours was complaining loudly about this - which resulted in the Egyptians closing the line they were in. All that did was back things up for everyone. Check on this, but I think we needed another Egyptian visa to re-enter the country. They are easily obtained before you go through immigration. It took a good 45 minutes to get out of immigration. All in all, I think we were into the airport by 10 pm.
We also had the 3 am departure to Milan for a 10 am connection to Newark. We arranged before we left for Amman to have a pick up service in Cairo. When we finally got through immigration, we were taken over to an airport hotel, where we got a drink and waited out the majority of the layover in the restaurant/bar. Our guy picked us up again around 1 am, checked us through and we went to the lounge for the last hour. Not much on offer in the lounge, but better than sitting in the gate area.
Hope that helps! Enjoy the trip - it was one of our favorites.
Cheers, Anne