While they are spot on with regards to the issues that they identify such as lack of multiple stations within Leeds, I think the solutions are unworkable in practice.
Putting a station or 4 tracking the viaduct east of Leeds will be very difficult and costly. The line east of Leeds is already incredibly short of capacity meaning that the stopping services often get delayed while letting though TPE services. As others have mentioned Wakefield is quite busy stop for London services so needs at least one direct train.
I personally think the solution to Leeds rail issues is a tunnel similar to that built in Leipzig. The tunnel would use the current freight line that diverges at neville hill and runs towards the River Aire where it will enter a tunnel. A first station will be provided at Leeds Dock. The tunnel will then join with a second tunneled route from Stourton and continue northward with stations at the southern end of the HS2 station, city square /classic station, Leeds Beckett Uni / General infirmary, Hyde Park / University of Leeds and at Headingly Stadia before joining the Harrogate Line.
Services off the Hallam Line, Castleford Line, York and Selby stoppers can all be run through the tunnel which could also provide direct semi fast services from Harrogate to Sheffield via Barnsley. Some services can turn back at Horsforth with some running through to Harrogate / York and potentially new stations at LBA, Otley and Ripon.
Four tracking would be provided between Neville Hill and Thorpe Park where fast services can use HS2 to travel to York.
The benefits of this scheme would be bypassing the area east of Leeds that is difficult to four track, providing multiple new stations in Leeds in areas that are hard to walk around due topography, providing more capacity for trains running to Manchester, Bradford and Skipton by diverting Harrogate and Hallam services away from the main station. A station at Headingly Stadia will also be more convenient for central Headingly than the current station.
This will cost a couple of billion but as far as I can think it solves a lot of issues with Leeds' current rail network and negates the need for a tram train that is being suggested currently for the Harrogate Line.