I've thought a bit more about this lately and this is how I'd propose to arrange the services once the planned upgrades are complete, with the aim of achieving a standardised half-hourly pattern wherever possible.
Starting with the Styal line, a mix of 4x fast and 4x stoppers seems sensible. The fasts go at 15 min intervals and are slowed down so that it takes ~15 mins to Piccadilly. Each stopper is sent out 4 mins after a fast service a takes ~22 mins, arriving at Piccadilly 4 mins before the next fast train.
That gives a turn-up-and-go frequency for local stations whilst keeping plenty of paths for long-distance services. I'd divide them up as follows:
2ph Local Airport-Blackpool
2ph Local Airport-Chat Moss (1ph Liverpool, 1ph Wigan via Golborne)
2ph Fast Airport-Preston-Scotland/Barrow
2ph Fast Airport-Victoria-Leeds-onwards
Then add 2ph Sheffield-Liverpool, 2ph Oxford Rd - Warrington and 1x freight to give a total of 13ph along the corridor. All trains would call at all stations through Castlefield, including Deansgate. This would help to maintain an even flow, spread out the loads slightly and also improve Metrolink connections.
Away from Castlefield, I'd use the 2x new turnbacks at Salford to terminate the 4ph Calder Valley trains which continue beyond Rochdale. That would allow a re-cast to setup a similar 4ph fast, 4ph stopper pattern from Platforms 5/6 at Victoria towards Rochdale, which becomes the terminus of the local DMU network. Atherton line trains would start from Southport and be timed to connect onto the Blackpools at Salford Crescent, reducing the impact of Southport losing Castlefield. Headbolt Ln becomes a shuttle to/from Wigan.
2ph Local Southport-Atherton-Salford-Victoria-Rochdale
2ph Local Blackburn-Bolton-Salford-Victoria-Rochdale
4ph Fast Salford-Victoria-Rochdale-onwards (3ph Leeds, 1ph Blackburn)
Platforms 3/4 at Victoria are then used for services from Chat Moss - the TPEs, a re-routed TfW Llandudno and the Northern Chester service which currently continues to Leeds. The new siding at Brewery Lane would be used for the terminating trains to layover as needed. Finally, there would be 2ph from Wigan NW to Stalybridge via Victoria, which has long been planned but never implemented.
2ph Liverpool-Victoria-Leeds-onwards
2ph Airport-Victoria-Leeds-onwards
2ph Wigan NW-Bolton-Victoria-Stalybridge
2ph Chester/Holyhead-Victoria
Overall this results in a more consistent, organised pattern compared to today. Stations towards Rochdale, Bolton and along the Styal line would particularly benefit from increased frequency. Plenty of loud opposition could be expected from TfW and Southport, but personally I think it's a price worth paying for a better overall service.
