Nevermind the deep state, here's the shallow but pervasive state
Brown on the Egyptian corporatism and the degree to which state institutions have gotten to define their own position in Egypt's constitutional debate, in negotiation with the MB:
But this is no long-term solution. It rests in part by awarding critical institutions more autonomy from external oversight than is appropriate in a democratic system. So the short-term problem may be too much autonomy for these bodies. Over the long-term, there may be the precise opposite problem: the autonomy of many bodies will rest on implementing legislation (for instance, the provisions for the Supreme Constitutional Court allow the current law to be maintained but do not prevent future changes in that law). A series of Islamist majorities might chip away at the freedom that state bodies now seem to think they may be achieving through the constitution.
So in the end, if things work badly, the result might look a bit more like the Mubarak regime than anyone now wants. Mubarak's authoritarianism was presidential and despotic to be sure, but it was not based on having the presidency micro-manage the affairs of various state bodies. Instead it was based on placing those bodies in reliable hands, coopting key members, and reining them in if they suddenly discovered ways to act too autonomously of presidential will.
If Egyptians are not careful they will slip back into that pattern. In the end, there is simply no substitute for healthy democratic competition.