Learning from our experience in Cairo, we actually went with a pre-packaged tour.
It's a generalization, but the much further you get away from Europe and North America, the more difficult it is to travel. And when we were in Egypt with a tour, we realized that you don't have to be on a huge tour bus with 60 senior citizens. We also learned that the amount of time you save with someone being at the airport to pick you up, making the hotel reservations, planning the itinerary - just saves a ton of time. We went with Namaste Tours. They took care of the hotels, breakfasts, some lunches and dinners, tour fees, guides, and domestic travel. We still had to cover our international flight, tips (which really added up), and food (which could be expensive if you did the touristy places they wanted you to go to). But in the end, we paid the tour company about $100 a day per person. So definitely the major expense was the air travel (no cheap flights around Xmas time).