At the end of the day, if you want a reliable, frequent, fast service you have to be willing to pay for it.
To maintain the current level of service reliably, Northern need to recruit many more staff, carry out maintenance more frequently and top up their order of 195's/331's. All of this costs money and the DfT is eager to reduce subsidies.
To run a reliable, low subsidy service, Northern needs to cut back on the amount of direct services and run branch lines as shuttles to a nearby station in say a reasonably populated town with good connections to IC services (e.g. The Windermere Branch)
The amount of services through the Castlefield Corridor needs to be cut too, unless the investment in 15/16 is to be made.
If so, I propose chopping the Crewe to Liverpool Lime St service in two and having the stopping Liverpool Section go from either Oxford Road bay or Manchester Victoria. The crewe section can start/end at Piccadilly. The Llandudno service can also start/end at Manchester Victoria instead of running to the Airport. Oxford Bay is also available
Basically end the madness of anywhere to anywhere, but in reality it being so unreliable a change or two probably wouldn't be the end of the world.
It's the triangle of rail service:
-Low Costs (either in subsidy and/or end user.)
-Reliability
-Frequent/Fast/Comfortable service
Pick two.