I agree it could be a problem, but I think the TPE issues are going to be ongoing for some considerable time, maybe on the scale of years not months (after all with a small break during covid its been ongoing for 5 years in May), and in that situation you have to look at what is needed v wanted. York/Hull -Manchester is a need, anything beyond that can be sacrificed until conditions allow the network to grow again. Maybe keep a couple of services a day to the outlying points to retain knowledge, and then when resources allow reintroduce a full service.
There is also the Huddersfield Dewsbury upgade in the pipeline, and that is going to further complicate matters. So TPE need to prioritise route knowledge over the Calder Valley route above serving places already adequately served by other operators.
As a passenger at Manchester if I am making for Newcastle, and there is a train to York I can complete my journey with some minor additional inconvenience, if however the next 2 or 3 services from Manchester north east are cancelled then I am going to be very late, and in all probability going to have an unpleasant journey as the train will be massivley overcrowded. (Been there, got that T shirt).
Given the current state of service and up coming works TPE should be taking a long hard look at what they do, and shouldn't be running any services beyond the core routes until the service on those routes reaches an acceptable level, and it is a very long way from that currently.
Prior to the meltdown in 2018 there were roughly 700 seats per hour between Leeds and Manchester each way throughout the day on the semi fast/fast services, the first goal should be to get back to that state or better on a consistent basis, i.e. with no gaps apart from during disruption unrealated to TPE issues. If that means fewer longer trains, and pruning the extremities thats fine, do it. Once that service pattern, whatever it looks like has run OK for some weeks or months and resources are in place, take the next small step, and if that doesn't work back track. Be very conservative in thinking to ensure resiliance, and make small incremental improvements. Once the service is seen to run reliably public confidence will return.
The south route is somewhat different, as Grimsby and Cleethorpes are much more reliant on TPE. Maybe run Cleethorpes - Doncaster as a shuttle and then run Doncaster - Manchester Pic as another service. Forget about Liverpool via the CLC or Man Airport, they are served by others.