Court of Federal Claims vs. GAO - Amazon vs. IBM

I am curious to hear reactions to the decision by the US Court of Federal Claims (No. 13-506C) in Amazon Web Services v. US and IBM, in which the court decided that the corrective action taken by the agency upon GAO recommendation was irrational because the GAO recommendation was irrational. I am particularly interested in knowing if you think there are things the agency could have done in its contract documentation, or in presenting its arguments to the GAO, to have brought the GAO to a decision in its favor under the original bid protest. Or is this a case where there is a difference of legal opinion between the GAO and the court that would have put the agency in the middle no matter what it did in its source selection process and documentation thereof. If the latter, it surely shows that source selection is a process fraught with peril for contracting officers.