According to Sam Laidlaw, appointed by ministers to look at why the franchise for the West Coast Mainline was such a £40m cock-up, the answer is – nobody really (see http://goo.gl/eg8pS for a report of his appearance before the Transport Select Committee). Certainly not ministers, who asked “penetrating questions”. And not the senior civil servants of whom these “penetrating questions” were asked, since they “had no reason to suppose the process was flawed as the lower levels were not escalating the problems to them”.
This is a tad unfair, as both Laidlaw’s Interim and Final reports ( see http://goo.gl/yWi8G) do a pretty clinal job in analysing what went wrong – the main culprits being a complex and poorly understood economic & financial model, and a management structure within the Department that simply did not work (post various reorganisations and cuts). Of course, given the “Francis Maude” view that Britain’s most senior civil servants deliberately block Government policies they do not agree with, one can understand if the DoT senior officials were reluctant to stand up & say that the changed franchise policy was an accident waiting to happen.
But if ministers have put into effect “in a rush” 
a policy (longer rail franchises) without ensuring they have the resources to implement it properly, don’t they bear some responsibility?
gleedsaling 