Egypt has large armed forces (450,000 troops), and lots of problems with leadership. In the Egyptian Army, like everything else in Egypt, corruption and favoritism are the most well-known and widely (if secretly) talked about problem. In the Arab world, and especially within the Egyptian military and security forces, almost nothing can get done efficiently, correctly, or on time without considerable wasta (an Arabic term, loosely translated, to mean "connections" or "juice"). The more wasta an officer or NCO has, the more success he has in getting things done his way. The Army's generals, obviously, have the most wasta, and can pretty much get anything they want done with a snap of their fingers.
While corruption and reliance of "connections" to get one's way in the military are well-known, other, even more troubling problems are plaguing Egypt's military and eroding its ability as a fighting force. For one thing, Egypt just wrapped up Operation "Badr-2010", five days of large-scale army maneuvers in the Sinai Desert. The exercise is the same thing it almost always is: Egyptian ground forces fighting a simulated war with the Israelis. The Egyptian stubbornly continue to make fighting a theoretical war with Israel the major focus of almost all their large-scale ground force exercises, despite the 30 year old peace treaty that has been in effect between Israel and Egypt since 1979. Furthermore, almost all of the major army units concentrate on training for conventional warfare.
Egypt has large numbers of special operations units, but for the regular divisions and corps of the Egyptian Army, very little instruction time is devoted to developing skills specifically for counterterrorism or anti-smuggling operations. Such training would be extraordinarily beneficial to the Egyptians, especially since their special ops forces are currently locked in a bitter struggle with Bedouin tribesmen, in an effort to wipe out the entrenched smuggling networks that have operated in the Sinai for years. With some preparation, regular units of the army would be better used supporting the Special Forces' offensive in the desert. Alas, most troops only train for potential war with Israel tomorrow at the expense of training to fight real enemies that are actually shooting at them today.
Finally, Egypt's considerable Coptic Christian minority (ten percent of the population) is grossly underrepresented, and often mistreated, within the Egyptian Army. Copts are often singled out for discrimination by the police and public in civilian life, but beatings, ill-treatment, and sometimes outright torture are becoming increasingly common among the Army's conscripts. Sometimes these beatings are motivated by a desire to force Coptic recruits to convert to Islam, sometimes they occur just out of discriminatory attitudes.