Egypt is beautiful but messy country. You will have to have plenty of patience and goodwill to deal with people and life organization. Let me start from the difficulties. 1) The hassle is really intense. The best is to ignore who is approaching you. Do not make even eye contact or try to be nice. There will be another person ten meters away trying the same tricks to convince to buy their goods or their services.2) The government really squeeze you out as a foreigner. They charge ludicrous prices for museums, sites and trains - avoid trains as much as you can, take buses, more comfortable and cheaper. The locals expect to cheat you and if you are not a good in bargaining you will pay ten times the fair price. It is true that what you spend in a day for hotel and travel is close to their monthly salary but sometimes it is just too much.3) There is garbage everywhere in the streets and locals have no sense of what a public good is.
There are many good things1) The archeological sites are amazing and to a large extent well preserved.2) If you get to know someone outside the tourist track, they are warm and kind.3) The Nile has a special feeling i did not find anywhere else except perhaps the Amazon.4) Cairo is chaotic but after a few days you end up kind of liking it with its the grandiose but dilapidated buildings, its relentless honking, and the infinite packs of stray dogs.
My favorites: Abu Simbel complex, Philae temple, Dendera temple, St. Catherine monastery.
My suggestion is to do the opposite of what normally people do. Meaning, fly directly to Abu Simbel (via Cairo) go to the site around 12-1pm when all the tour buses are gone, sleep overnight there and then take the bus the next day to Aswan. From there, after seeing Philae and the Nubian museum, and depending on your time, slowly move up to Luxor with intermediate stops (Kom Ombo, Edfu, Esna) and beyond (Dendera, Abydos). If you want to take a felucca ride on the Nile do it in Aswan, it is much more pleasant. In Luxor, avoid organized tours to the sites. You spend most of your time waiting for someone who is late, someone who has interests opposite to yours, or in alabaster shops and lunch restaurants. I mostly walked to where i wanted to go. It is a long walk (from the west pier where the ferry arrives, it is 9 km to the valley of kings and 6 km to the valley of queens, from my hotel to the Karnak was almost 4 km) and , if it is hot, it maybe unpleasant, but you can take your time wherever you feel like. Be aware that most of the remains are not on the sites: you see the buildings and the colors, can try to imagine what it was like there, but that is all. The sunset from just outside the souk in Luxor facing the Luxor temple was amazing.
A warning: in the Valley of Kings and of the Queens they let you see only three tombs, and guess what, the most beautiful ones can be visited only with an additional ticket, whose price is astronomical. Seti I tomb was 40 US dollar. Nefertiti tomb 50 US dollars but it was closed. Another warning: if you want to take a break on the Red see do not go to Hurgada. It is just an endless strip of resorts. I would suggest the gulf of Aqaba between the Sinai and Saudi Arabia - avoid Sharm-el-Sheik for the same reason you want to avoid Hurgada.
The Giza complex is awesome but the crowds are extraordinary. Again use the trick of going at midday when most of the buses are gone. Avoid camel rides, horse rides, and all the typical tourist traps.There is an extra ticket to enter the pyramids, but after you have seem Abu Simbel and the the Valley of Kings, going inside it is not worth.
The Grand Egyptian Museum is a bit of a rip off. You pay 25 USD to enter but then they tell you the Tutankamen room is closed. The museum is new and very nice but i am not sure the organization of the material is ideal. Incidentally, I found the Nubian museum in Aswan and the Luxor museum smaller but more pleasant to visit.
If you have time take a ride to some oasis (Dakhla, Siwa) and spend a day there doing nothing like the local do. It gives you a different perspective on life😄. And if you have time go to the Sinai and visit St. Catherine. It is a special place even for people like me who are not religious. Just the sheer views and the mountains make it worth a visit.