If there are truly free elections, the Muslim Brotherhood will win again.
Again...
Top three finishers in the first round of Egypt's 2012 presidential election:
Morsi 25%
Shafik 24%
Sabahi 21%
And then in the runoff:
Morsi 52%
Shafik 48%
And that 52% in the runoff included the votes of many secular liberals who were afraid that a vote for Shafik meant a return to military rule and the days of Mubarak. If they're more sympathetic with the military now, then I don't see how another Muslim Brotherhood candidate could win. You might still have someone with Islamist leanings, but someone backed by the MB itself seems unlikely.
In the parliamentary elections, the Muslim Brotherhood and the Salafists won almost 2/3rds.