The best case I've seen for this project mentions that this will give greater capacity for rail passengers. This will then in turn potentially free up routes for Freight rail traffic.
A problem on the railways currently is that Passenger trains take precedence over freight trains which often have to wait in sidings for the passenger traffic to go through. This 'parking' happens regularly near me on the local railway. Such delay hinders rail freight development in England especially, I think.
Now others have written that this great amount of money needs to be spent on local networks. That is true, especially in the north for example the Liverpool - Manchester - Leeds/Sheffield - Hull route needs such upgrade. However do we really thank that this government, if it were to cancel this project, would spend that many on the North?