I got back about a month ago from a trip to Egypt after soliciting a lot of advice off of this forum, and I just wanted to post a few responses for future travelers.
We traveled to Luxor via the overnight train from Cairo. It was very nice, and easy to sleep on (for a train) and felt very safe. It was a few hours late but it seems everyone in Luxor knew that would happen.
While I am usually an independent traveler, I only had two days in Luxor so I decided to book through Flats in Luxor. I think this was a very good decision, because it allowed us to see all the sights without tons of stress. We would have not been able to do it without an organized private tour.
I would like to emphatically recommend our tour guide, Hussein. He is a freelance tour guide that Jane hires at sometimes, but I would whole heatedly recommend requesting him. He is extraordinarily knowledgeable, I have taken college courses in egyptology and he was really able to expand my knowledge. He was also very nice, friendly and not pushy at all. He never brought us to a "perfume shop" or "alabaster shop" or what have you (though offered to take us if we wanted). He also knew everyone working at the sights and had friendly relationships, making the experience very positive. We found that one of the most difficult parts of traveling this region is constantly having to say no to people, creating a general negative vibe with everyone competing for your money. Hussein protects you from all of that and allows you to have a really lovely trip.
Over the two days we saw 6 sights. Honestly, my favorite places were tomb of the nobles and tomb of the artisans. We were in those little tombs alone, and they hadn't been ruined by vandals or used as churches. Not to diminish how amazing the valley of the kings is, but these were really mesmerizing.
I enjoyed having lunch at Jane's it was one of the few good meals I had on my trip. Make sure to remind her if you are vegetarian. Also note that she expects her payment in cash when you arrive. Although, I would wait until the driver she has arranged for you picks you up and ask him to take you to the bank so you feel safe. (Perhaps she wouldn't like this, I think she was annoyed, but as a young woman I didn't feel comfortable walking around with that huge amount of cash)
It was really great but not somewhere where I would want to spend a week. However, maybe people who did stay longer found lots to do.