Mixing the more-or-less totally separate Merseyrail system with other lines is not a good idea.
However, what about splitting the stopper services so that they cover metropolitan areas? What I mean is, instead of having a stopper going from Liverpool Lime Street to Manchester Victoria, have an extra one going from Lime Street to Warrington Bank Quay and another one going from Bank Quay to Victoria. This way, it's clear that if you want to go from Liverpool & Manchester, you should use the faster services. I know that this would not be without complications in 2011, but perhaps after electrification, the northern hub improvements and hopefully, some four-tracking and passing places for fast trains, as well as more fast trains per hour, this may be possible.
Also, if all the long distance services are re-routed away from the CLC route, then perhaps the Merseyrail Northern Line could be extended from Hunts Cross to Warrington Central, with a Northern stopper service (perhaps under a TfGM scope, maybe even branding) could do Warrington Central to Manchester stations.
Sorry for the lack of clarity, this is basically what i proposed.
I.e. services on the Mid Cheshire line & lines out of Lime Street would be all-stoppers, but terminate at the respective boundaries of the commuter areas.
So, taking the Manchester-Liverpool line, you would have for instance
GMPTE:
Manchester Picadilly-Warrington Central (all stops)
Manchester Victoria-St Helens Junction (all stops)
Merseyrail:
Liverpool Lime St-Warrington Central (all stops)
Liverpool Lime Street-Warrington Bank Quay via St Helens Junction (all stops)
Northern Regional
Stockport-Liverpool Lime St (Piccadily, Oxford Rd, Irlam, Birchwood, Warrington Central, Sankey, Widnes, Liverpool SP, Liverpool Lime St)
Rochdale-Liverpool Lime St (Victoria, Eccles, Newton le Willows, St Helens Junction, Huton, Liverpool Lime St)
Northern Intercity
Hull-Liverpool Lime St (Selby, Leeds, Huddersfield, Victoria, St Helens Junc., Liverpool Lime St)
Newcastle-Liverpool Lime St (Durham, Darlington, York, Leeds, Huddersfield, Piccadilly, Warrington Central, Widnes, Liverpool SP, Liverpool Lime St)
with regard to the question on the Mid-Cheshire line, this was a suggestion that the GM rail operator would run a Northwich-Picc. 'all shacks', and ATW/Northern Regional a semi fast to Chester via Northwich, which could extended to Llandudno or elsewhere.
This would also be covered by the 'Northern Intercity' to Holyhead, which would call:
Selby, Leeds, Huddersfield, Victoria, Warrington Bank Quay, Runcorn East, Chester, Prestatyn, Rhyl, Colwyn Bay, Llanududno Junction, Bangor, Holyehad.
Similarly the Liverpool-Crewe service would be an 'all shacks' stop, with the Birmingham service continuing under LM or ICWC.