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The North hardly gets the crumbs from London's table. I think we can all agree that DfT, based in London, only look at the country from within the boundaries of Greater London and the Home Counties.
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That is clearly not true.
There was a problem with the modelling which is used to predict demand and growth, but that I understand has long been addressed. The issue was that the model made assumptions about network topology that did not apply to mesh-networks and as a result underestimated demand in provincial centres, not just northern cities.
The trouble has been that patronage has not been at sufficiently high enough level on specific route sections to justify investment. The matter is complicated by the nature of the network with benefits of improvements being shared across multiple routes and frequently not achieving a critical mass around BCR.
By substantial improvement in efficiencies it is hoped that better returns on investment can be achieved, and thus having a more positive impact. The problem will not be resolved however until patronage is at a sufficiently high-enough level that the high levels of subsidy can be cut. There are specific sections where capacity is constrained and unable to service future projects, but they are (mostly) already being addressed.
What has not helped has been the false-hopes given by specific politicians, and the twisting of facts by activists for political means unrelated to serving either the travelling public or the tax payers.