It is curious that President Obama thought it necessary to interject his own remarks to an American audience after Mubarak had announced that he wouldn't run for re-election. He didn't endorse or gainsay the idea that Mubarak would preside over an "orderly transition" and not stand for re-election. He piously proclaimed that, whatever the Egyptian people decided, the U.S. would continue to stand in support. Perhaps motivated by simple narcissim, some of what he said might be counterproductive.
Now, the best thing for peace and stability in the region is for the military to assume an important role so as to preclude the dominance of the Muslim Brotherhood or even the broad "democratic" will which is anti-American and anti-Israel and will almost certainly jeopardize the peace agreement of thirty years' standing. This would require some time for such a transition to be effected. Obama has essentially committed himself to continuing support ( presumably the aid that he threatened to withdraw if Mubarak didn't do the right thing ) even if the rule in Eqypt becomes quickly Islamist and radicalized. Precipitate action has invariably led to takeover of revolutions by more radical elements. (Cf the Bolsheviks taking over from the Mensheviks, Nasser taking over from General Naguib, Saddam Hussein taking over from those who overthrew the Hashemite king of Iraq, ...even the Ayatollah taking over from the immediate revolt against the Shah and the interim rule of Baktiar.
It has been only the military in Muslim countries that has prevented the otherwise inevitable drift to Islamism. Turkey has only recently, after almost a century of military-led restraint, turned Islamist. Likewise, Algeria and others.
Obama is likely to follow in the footsteps of the feckless Carter, who turned a stanch Iranian into a committed and lethal enemy, and preside over the transition of Egypt from friend to foe, likewise.
Once again, Israel will see the folly of trading a piece of paper for tangible resources. Only between stable democracies, can treaties be counted upon to mean something after the passing of those who signed them ( although, even here, Obama and Clinton have abrogated some agreements put in writing by Bush.)