I have no opinion nor enough knowledge to have an opinion on how directly responsible Shinseki is for the VA problems. In general I do think we don't have enough of a tradition of honorable resignations, in which the people in charge take the fall simply because they were in charge. I think when such resignations happen more commonly people understand that they're somewhat symbolic. The point isn't "I am horrible," but instead, "this is just unacceptable." The resignation acknowledges that.
