The positive elements of large organizations; the ability to mobilize large numbers, access to funding, a reliable support infrastructure, etc; are unfortunately offset by tremendously negative (and inevitable) flaws.
Large organizations are primarily dedicated to their own perpetuation, because they wrongly equate the reason for which they exist with their existence itself. In other words, they begin to believe that their cause and their organization are one and the same thing. It is once the organization reaches this point of confusion that they cease to be genuinely useful, and very often, become an obstacle to the cause they were created to serve.
In the case of revolutionary organizations (which is really an oxymoron), their most important means of leverage in their relationship with the power they oppose, is their ability to control opposition. That is, their capacity to de-mobilize their supporters in exchange for concessions from power. The reality is, both their mobilization and their de-mobilization are nothing more than tactics to improve their position to bargain with power; not to overthrow it. Never mind their rhetoric.
They are not actually interested in fundamentally changing the system, because they are an integral part of the system, they operate within it, are invested in it, and really fundamental change is as much against their interests as it is against the interests of power.
If there is any question about whether or not the larger opposition groups in Egypt will negotiate with the regime, or already are, the answer is: That is what organizations do.