You have to travel on this line to appreciate the sorry state of affairs. I am not aware of any major subsidence issues currently- the slow journey times seem mainly due to timetabling. Over the part of the route not shared with other services (i.e. Moorthorpe-Sherburn) there seem to be hardly any passengers.
On my last journey, last year, the first southbound train carried approx. 6 or 7 passengers when it arrived at Pontefract where a couple joined and a couple alighted. The train then sat for 6 minutes waiting departure time. It ran with this light load to Moorthorpe where it again sat for 6 minutes waiting departure time. At subsequent stations to Sheffield more passengers joined but it could be argued they could have used the other services using the line.
The returning northbound train had a similar load into Pontefract and similar joiners/alighters. At Sherburn the lady guard came round the train and told us not to worry that the train was standing at the platform (where no-one joined or alighted) as it wasn’t booked to depart for 7 minutes.
I haven’t used the service this year but the timetabling issue still seems to exist Thus looking at Realtime trains for 13 February the equivalent southbound train sat 7 minutes at Pontefract and 6 at Moorthorpe. The Northbound return recovered 2 minutes lateness between Pontefract and Sherburn, then sat for 4 minutes at Sherburn.
Mention is made of use of the line by freight. However again looking at Realtime trains for 13 February only 10 freight trains used the route and these were all in night time hours when presumably paths might be found on alternative routes.
As stated by others, you can travel from York to Sheffield by the faster, more frequent and more comfortable Cross-country service. All the communities on the route can access the national network by using other frequent services and changing at the likes of Leeds Doncaster or Sheffield. The only unique contribution made by the route (providing a quicker link Moorthorpe-Pontefract-Sherburn) doesn’t seem to have sufficient users to make it worthwhile. The first question is- is the low usage because there is no market, or because the service is so poor, or a combination? The next question is if you had some spare resource would augmenting this service be a better use than other alternatives. Thus Barnsley and Castleford don’t have a through service to York but they have bigger populations and bigger potential. Passengers from Pontefract can access Castleford easily. Perhaps the service should be rerouted to serve Barnsley and Castleford (as suggested by Billio and others above).
I am surprised no-one has brought up the possibility of running a local service on the Knottingley-Doncaster line. This would offer much faster journeys from Castleford/Pontefract to Doncaster and hence London and could be combined with the clear need (mentioned by johntea above) for an augmented Leeds-Castleford/Pontefract service. Would seem to be much more use than the proposed extending of the Pontefract-Wakefield service to run to Leeds via Westgate