Way cool web site alert! We apologize to Andie for not mentioning this site sooner, but it's really excellent: Prehistoric and Predynastic Egypt. It's very well designed and has a great deal of accurate and useful information. Visit there often.
Again, we reiterate that the prehistory of Egypt does not begin with the pyramids. There is a lot of interesting archaeology predating Dynastic times. In most areas of the world, the Predynastic material of Egypt would be considered a major source of archaeological knowledge (which it is increasingly becoming), yet especially the prehistoric is often ignored. There are some good reasons for this, apart from the usual human tendency to pay attention to WAY COOL STUFF at the expense of other things. Part of it has to do with history, part with geology. Historically, archaeology developed out of a desire to fill museums with objects that people wanted to (pay to) see. Obviously, Egypt provided this kind of stuff in spades.
On a more natural level, Egypt is somewhat unique in that about 90% of the country is uninhabitable, the old "Gift of the Nile" schtick. Consequently, every square inch of the narrow strip of land on either side of the Nile has seen almost constant occupation for thousands of years. This means that all of the early stuff has been deeply covered up by later habitations. Add to that the fact that the Nile has been prograding (building up sediment) since the end of the Pleistocene (ice age) and you have very little early material that is within shouting distance of the surface.
On the other hand, the desert does often give up very early remains since over the course of the last few hundred thousand years (including the relatively recent past) the desert areas were habitable and, as a consequence of being deserts today, a lot of this material is just lying about on the surface. That in addition to the preservative powers of the dry desert itself.
End of ramble.