We just flew EgyptAir last week between Cairo and Larnaca Cyprus. This was an international flight, so we got to enjoy the new international terminal in CAI, which is actually quite nice. I've been through Mumbai, Delhi, Hyderabad and Bangalore India (4 of the worst airports I've ever seen in the world)- Cairo was a dream next to them. In fact, the new terminal is nicer than JFK or MIA. That said I'm not sure about the domestic terminal. But overall the immigration, baggage claim and then check in for our outbound flight were not bad. Either we got lucky or the stories about Cairo airport are overblown. We did have interesting experiences with people cutting in front of us in line and sitting in our seats (until we had the FA ask them to relocate).
As far as Y vs. F, our flights had a big differential in price, so we opted for Y. We wound up getting exit rows in both directions, which were great. The planes are old, very old 737's and the food is terrible. In F you get a bit more pitch and 2x2 seating. You will probably also have the F cabin to yourself, our flights were very lightly travelled and I think F was empty. Although $20 goes a long way in Egypt, I'd probably would have opted for F if that was the price difference on our flights.