I have no particularly privileged insight into the inner decision-making of the Muslim Brotherhood, other than meeting with its leaders, including Khairat al-Shater, on a regular basis and seeing rank-and-file and former members quite often too. As someone who has followed the group for almost a decade now, I don't think the answer to why they decided to run Shater now lies mostly within the organization and its logic. It has to do with the political environment and developments in Egypt's transition in the last few months, and especially the fact that this ill-thought out transition (for which the Brothers deserve a good part of the blame) is coming apart as it reaches its end with the presidential election and the drafting of the new constitution. I talk about that in my latest column for The National.
Shater's candidacy is something that has been envisaged for six months at least — since the beginning of the end of the entente cordiale between the MB and SCAF. The decision to go for it was probably made by the top leadership (the "gang of six" led by Shater) in recent weeks, but not sold to the broader leadership in the Shura Council until Saturday — and then barely so if the reports that the Shura Council approved the decision by a margin of only two votes is true. I would argue that this decision was made because of several overlapping concerns, which we might conceptualize as four concentric circles of variables.