Generally he did not promote out of normal order, so he cannot be accused (though he will be anyway) of favoring Muslim Brotherhood officers. On the other hand, some of the promotions do show forethought. The promotion of Military Intelligence chief Gen. Abd al-Fattah Sisi to the Defense Ministry only days after retiring General Intelligence chief Murad Mowafi, may show a tilt away from the once powerful General Intelligence Directorate and towards Military Intelligence, And the fact that one key SCAF member, Gen. Muhammad al-Assar, was retained and promoted is of interest, as he is the Defense Ministry's American liaison. His retention may help assure the US supports the changes. (It will also fuel the conspiracy theorists — a mix of the American right wing and the Egyptian left wing — who think that the US supports the Muslim Brotherhood).
It was a stunning move and still may lead to a confrontation with the Supreme Constitutional Court, though the appointment of a respected jurist as Vice President may be intended to pre-empt that. Morsi has apparently kept the Army as a whole on board by retiring the senior generals with respect (Tantawi and Enan get the Order of the Nile, jobs as Presidential Advisers, and, implicitly, immunity from prosecution for actions during the transitional period; the second echelon stays loyal as they become the first echelon, speeded by the long-overdue retirement of Tantawi and the early retirement of the others; but the military has clearly been subordinated to the civilian sphere.
Or at least that's how it looks so far.