When visiting the various sites any type of footwear can be worn, but ladies should avoid wearing high heels due to the sandy conditions (Egypt is a desert country) and the unevenness of the floors, especially when wooden floorboards have been installed as heels could get trapped and/or broken between the planks.
Cotton is by far the best fabric to wear as it tends to keep you cooler than acrylic clothing, especially if you are going to be spending a lot of time in the sunshine when visiting sites. Skirts are okay to wear, but remember that some places will require you to climb stairs, so a little bit of decorum should be considered and perhaps jeans could be the best substitute.
When visiting mosques you will be expected to remove your footwear, though some of the larger mosques do supply paper overshoes. Please be prepared for this and follow what you are asked to do. Likewise women are usually asked to cover their shoulders and upper torso’s so if a mosque is on your itinerary for the day, think of dressing accordingly.