Aqaba is really only the gateway to Petra - there is a courtesy bus, but it drops you a mile past all the really interesting shopping area in the middle of nothing - so save your energy unless you want to get a taxi to the main 'real people live and shop here area'. Petra is a must. It's quite a long haul and fairly rough walking in places, so wear really comfortable shoes and take hat/water etc.
The trip to Cairo from POrt Sokhna is long. The pyramids were fantastic; but yes you will be plagued by kids trying to sell you stuff. Head down and no eye contact. We did the trip that included the Muhammad Ali Mosque and River Trip - both were good but not exceptional. The mosque is huge and could be beautiful, but it needs a real good clean. I asked our guide why in a moslem country the house of Allah was so unkempt and he just shrugged. We didn't bother with the extra £6 to go inside the pyramid (not for the claustrophic) and were told we didn't miss anything.
If you are of a sensitive disposition, beware that Cairo is pretty much all slum and there are some unpleasant sights out there. The pollution is thick - both in the air and on the ground, and especially in the Nile and its canals.
The trip to Luxor from Safaga is even longer so take pillows if you can. You get a picnic box on all the trips (even though you get a proper lunch), so water/drink, nibbles etc. are to hand. This is a 3.5 hour drive EACH WAY - take books, iPod etc. as some of the landscape is boring. Luxor was great. Valley of the Kings is the pinnacle so if you don't do any other trips do this one. Karnak also amazing.
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