There's nothing wrong with comparing the emerging costs of a project with the firming up benefits and asking if it's still worth doing. If it's not worth doing then spend the money on something better. I cant imagine anyone disagreeing that shortening journey times and improving capacity are laudable, but £3bn for 3 minutes and a couple of extra paths? Spending millions at places like Ravensthorpe to put in a flyover to avoid conflicts with the hourly Wakefield trains which probably don't have much more than a dozen passengers on them. Barmy. Network Rail have let the project spec run away again.
Using a figure of £1m per single track kilometre which the recent RIA report suggested was an achievable cost, then spending £3bn would pay for electrifying (if my maths is ok) over 900 double track miles of electrification. Manchester to York, Hull and Middlesbrough, the Harrogate loop, Liverpool to Doncaster via the CLC and Hope Valley, Windermere Branch, and Carnforth to Barrow total only approx. a third of this. Much better ways of spending.