When you look at all the most punctual, successful rail networks in the UK, such as Merseyrail, London Overground, the Glasgow suburban network, they all have one distinct thing in common: trains go on routes and stick to them! The current Southport situation is the equivalent to Merseyrail's Hunts Cross services being split three ways between Ormskirk, Headbolt Lane, and Southport, which doesn't happen, because it's inefficient. I'm sure many people from Headbolt Lane and Ormskirk would like a direct link to Hunts Cross, but in practice, its impractical to have infrequent services from all three branches serving Hunts Cross.
The current arrangement on the Wigan - Southport line involves 2 Southport bound trains being just 15 minutes apart, followed by a 45 minute gap, which is wholely caused by the path onto the Castlefield corridor. If both Southport trains went through Victoria, they could be more evenly spaced, appropriate for an outer suburban service. I would propose something like this:
1tph Southport - Leeds via Atherton, DMU
1tph Southport - Blackburn via Atherton, DMU
2tph Stalybridge - Wigan NW via Bolton, EMU
1tph Headbolt Lane - Wigan, extending to Oxford Road or Victoria via Atherton semi-fast in the peaks
This way, both Southport services share identical routes as far as Todmorden on the Calder Valley line, in the paths of the existing Wigan/Headbolt Lane trains, providing an even, 30 minute spacing.