Egypt looks certain to have a change in President as a result of the current protests, which is all to the good. But if you ask me, countries in this situation should also strongly consider doing away with their dictatorship-enabling presidential systems.
The problem with a strong president, especially in a country that doesn’t have a stable tradition of political parties or peaceful transfers of power, is that there can only be one. The whole country is plunged into a winner-take-all political contest. If the winner turns out to be someone with a “one man, one vote, one time” concept of democracy, then that’s all she wrote. And if you suspect your opponent is someone with a “one man, one vote, one time” concept of democracy, then you’ll feel it’s both prudent and necessary to really push the envelop in search of your own victory. And of course if you’ve got that figured out then so does your opponent. It’s a recipe for suspicion and abuse.
By contrast, a system oriented around a parliament elected with some form of proportional representation is going to set the stage for new round of bargaining among political elites. That doesn’t guarantee a good outcome, but it does militate in that direction.