In my opinion the Don Questo is the best ship in the Sudan. It sticks out from the other ships in a few ways, so you'll have to make your own decision in what is important to you.
Don Questo is not luxurious in the way it looks. The cabins are small and most have no porthole. No toilets or showers in the cabins. They do have a washbasin. Most other ships will have more luxurious cabins.
The ship is an English built steel trawler, later tranferred into a oceanographic research vessel. That is when the big water tanks came in. After that she was changed into a scuba dive ship. It is a sturdy and good ship, with an excellent crew.
The engines give her enough power to travel quickly, so it is possible to go to places where the other ships don't get easily or not at all.
The generators are also very powerful. This makes it possible to fill up all bottles 5 times a day in very short times. It gives you the chance to make more dives than is possible on other ships.
The crew is very good, not only in handling the ship, but also in handling the passengers. If you happen to be the only one that wants to do a nightdive somebody will just take the zodiac, bring you, wait for you and get you back. Dinner will be arranged so that you will not miss it.
As for the food: you won't find better food on any life aboard, and I may as well include most restaurants too. One of the owners used to be a chef, and he believes that one should have a two course lunch, three course dinner and have a variety. Ever heard of a life aboard where they will ask you whether you want your steak medium, rare or well done? The owner knows I don't like shrimps, so I get something else instead without even having to say something.
They have a new cook for a year now. The old cook was excellent, and this one is almost excellent too. Only his cake was not (yet) like the previous cook did it.
The Don Questo is changing every year. They make improvements, and also listen to what the divers say. It is not the same as it was when I was there the first time (with Christian here two post above me)
This became a long story. If you want to see the ship look at my website. You will find two series about the Don Questo and Sudan underwater pictures. For Sudan land you will have to check the sections "living" and "nature"
One more thing about the flights: you don't have to go through Cairo anymore. KLM and a few other airliners flie from Schiphol to Khartoum. From there you can take (the same) plane to Port Sudan.
The Sudanese ambassy is in Den Haag for your visa.
Perhaps I will see you there, I am thinking of going there myself again around that time.