I think Warrington is key to any changes to the CLC line. It's 4 stations have more passengers than the rest of the non-Merseyrail stations put together. It's main station gets 4 tph to Liverpool and Manchester from the current arrangement, which is all it'd probably get with a split service, but with semi fasts and direct trains across the Pennines. They'll also be keen on retaining links from Birchwood and Padgate to Liverpool and Warrington West to Manchester.
Warrington hasn't thrown its lot in with Liverpool or Manchester in the devolution deals, preferring a Cheshire grouping it will presumably have a big influence in. I doubt they'll be keen on anything perceived not to benefit Warrington.
I'd also question the value of more stops at the small Greater Manchester stations, and also how Mossley Hill and West Allerton would be served - LM won't want them and neither should Liverpool want its already slow service to Birmingham slowed further. Halton Curve maybe?
Warrington has grown dramatically over the last 15 years from an Economical point of view primarily because of its closeness to the Motorway crossroads of the M6 and M62 . As a result, its traffic problems are drastic and currently not sustainable. It's linked to the economies of both Liverpool City Region and Manchester City Region. With Halton throwing its hat in with LCR I would of thought greater integration with either MCR or LCR would have been more beneficial.
If anybody doubts the point of Hunts Cross, look up its passenger usage statistics.