I did Northern & Dahab with redseaexplorers.com and enjoyed it very much. GUE infested but openminded, sidemount / rebreather / double tank / freediving friendly. Trimix, DPV, Nitrox, ... Started from Hurghada.
I've seen the MY Blue but wasn't on it. Very different focus; no tech diving, no deco diving, focus on luxury on the boat for the recreational diver. Your choice.
Northern / Dahab: reefs and wrecks, but no sharks
Southern / Sudan: Sharks and reefs, mantas and dolphins, but only few wrecks
I did a 7-day river Nile cruise many years ago, it started in Luxor, went down to Assuan, a day trip by bus to Abu Simbel, then back to Luxor by ship. Then flew to Cairo for another 3 days for the museums and pyramids. Was a great trip. I don't know if cruise ships go from Cairo all the way to Assuan, it's a long way. The interesting part of the river Nile cruises is between Luxor and Assuan.