My choice would be Option C, especially since it would improve the service on my local line (the Mid Cheshire)
But I think it will encounter a lot of political opposition, because of the large number of users who would lose direct services and/or have increased journey times. In timetable recasts, the loud complaints from losers always drown out the faint praise from gainers.
I have tried to summarise below all the losers, line by line:
CLC line:
• Loss of direct service Liverpool – Airport (change at Oxford Road)
• Loss of direct cross-Warrington service for the lesser stations (change at Warrington Central)
• Some lesser stations have increased journey times to Manchester (all shacks)
Chat Moss line:
• Loss of direct service Liverpool – Piccadilly & Airport (change at Oxford Road)
Wigan lines:
• Off peak, reduction from 3tph to 2tph on the Atherton line (already cut from 4tph!)
• Loss of direct service Southport – Piccadilly & Stockport (change at Bolton or Salford Crescent, and at Piccadilly for Stockport)
• Off peak, loss of direct service Southport – Oxford Road
• Off peak, loss of fast service Wigan NW – Piccadilly & Airport via Chat Moss
Bolton - Chorley - Preston line:
• Loss of direct service Blackpool – Stockport (change at Piccadilly)
• Off peak, loss of direct service Preston – Salford Central & Victoria (change at Salford Crescent)
Blackburn – Clitheroe line:
• Increased journey times to Manchester via Bolton due to calls at Moses Gate, Farnworth and Kearsley (DMU stoppers on electrified line!)
Hazel Grove line:
• Loss of direct service Hazel Grove – Bolton, Preston & Blackpool (change at Piccadilly, main shed to P13/14, or at both Stockport and Piccadilly)
• Off peak, reduction from 3tph to 2tph (wires to Hazel Grove only used in peaks!)
Stockport – Crewe line:
• Loss of direct stopping service Stockport/Cheadle Hulme/Handforth – Chelford/Goostrey/Holmes Chapel/Sandbach/Crewe (change at Wilmslow)
Sheffield via Hope Valley line:
• Loss of direct service Cleethorpes/Sheffield – Airport (change at Piccadilly)
Huddersfield - Leeds line:
• Increased journey time Piccadilly – Hull (all shacks Stalybridge – Huddersfield)
• Peak only, reduction from 2tph to 1tph on Ordsall Chord (Victoria – Piccadilly & Airport)
Chester & N Wales lines:
• Increased journey time N Wales – Manchester (slower direct service to Piccadilly via Northwich, or change at Chester for Victoria via Warrington)
• Loss of direct services N Wales & Chester – Oxford Road or Airport (large increase in journey times)
Altogether that is going to add up to a lot of aggrieved users kicking off!