The problems at Leeds are common to a lot of other places north of Watford and the solution isn't to build a 12 track viaduct costing ££bn.
Too many tiny trains.
London gets the money because the trains are maxed out on length and height so you can only add capacity be removing seats, adding a second deck or digging new tunnels. This simply isn't true in Birmingham, Manchester, Leeds and others that are plagued by 2-3 coach micro trains.
Looking east, the off peak pattern is 9tph 4x TPE from York - 2x Newcastle, 1x, Scarborough, 1x Middlesbrough then a fast Hull, slow Selby, 2 more Northerns from York one fast, one slow and 1 XC.
This is not especially high density for a 2 line railway, but already far more than what is needed and not one of is them anything close to 'full length' - does Newcastle - Leeds really need 3tph and a fourth from Middlesbrough? The timetable needs what Gardeners World might call a rejuvenating prune.
The stabling in west facing platforms is far from ideal. Aside from the narrow car park it is tricky as the old vacant plots around the river to the north of the site also happen to be prime city centre development land. There are probably easier options like shipping sets off to Huddersfield, Bradford or Wakefield between the peaks if they really can't get to Neville Hill or Holbeck but again a more disciplined approach to network capacity is required to force down less palatable options rather than offer something to the operators that works on paper but not in real life.