Andy Drukarev sat down with Shaw and posted this Q&A about the decision. I think it provides quite a few insights. Shaw mentions several times that Brett "caught up" or "closed the gap." It sounds like Josh had the edge going in, but that the coaches wanted to give Brett a good look because of his talent.
http://stanford.rivals.com/content.asp?CID=1399338
http://stanford.rivals.com/content.asp?CID=1399338
