I can understand capacity issues, and that was my first thought with regards to the ECML, but "refused the application for reasons that included protection of the revenues of Virgin Trains (the incumbent inter-city operator on the WCML)"? 

We're seriously knocking back an application for passenger choice, based on protecting profit of a private company?

ECML may be a different kettle of fish, as the new top speed, and the non-stop Newcastle to London services, may be exactly what the Tories are looking for in their infrastructure plans. High speed link, and someone else is wanting to pay for it!