The decision to come with its own candidate is a dramatic shift of the former position of the Ikhwan, which after the fall of Mubarak said that it would not field its own candidate, sure as it was to be able to score a big victory in the parliamentary elections. But it seems that the Brotherhood after all got worried that its strong position in parliament wasn't a guarantee that it would be able to exercise enough power. First it became apparent that there were strong differences of view between the Ikhwan and the military as to what extend parliament could have its way.
"We have witnessed obstacles standing in the way of parliament to take decisions to achieve the demands of the revolution," Reuters press agency quoted Mohamed Morsy, head of the Freedom and Justice Party, the political ar of the Ikhwan."We have therefore chosen the path of the presidency not because we are greedy for power but because we have a majority in parliament which is unable to fulfill its duties in parliament," he said announcing the decision to back Shater. What Morsy did not say, is that the Ikhwan is increasingly opposing the government Ganzoury. The fact that the military leaderschip keeps on backing the government and is standing in the way of the aim of the Ikhwan to form a government that is based upon its own parliamentary majority, seems to be the main reason for the decision to make this bid for the presidency.
Another reason may have been the rather strong performance of a some candidates that cater for the same constituency as the Ikhwan and in doing so seemed to jeopardize the Ikhwan's strategy. The Brothers are in particular worried by Abdel Moneim Abul-Fotouh, who, after he in an early stage defied the wishes of the Brotherhood and announced his candidacy, was expelled for the Ikhwan. The other is the Salafist preacher Hazem Salah Abu Ismail. Both of them are showing a growing support among the younger ranks of the Ikhwan in recent months.
(Amira al-Howeidy of Al-Ahram Weekly wrote a good portrait of Al-Shayer that can be found here)