I can confirm Ellesmere Port is a rather quiet station in Merseyrail terms, despite being within walking distance of the town centre. The car park is fairly decent sized, however as other posters have pointed out it’s not in the nicest of places and there have been many issues of youths/little w*****s vandalising station facilities and threatening the public and rail staff.
Hooton is near to a motorway junction, has an enormous car park, which is I believe only £1 or £2 for a day. Despite being in the middle of nowhere, it is a very busy ststion, especially on Saturday, when from personal experience I can say it gets so busy that one member of staff can struggle with the volume. As well as Ellesmere Port, it also serves as a park and ride for Flintshire.
As for Stanlow and Thornton, I can see it being mothballed, similar to IBM or Redcar British Steel. Northern did do a return journey to Leeds which lent itself to commuting to Warrington and Manchester, and that did attract some passengers from the port. The two shuttles a day now to Helsby are a little useless. The first does stsrt from Lime Street I believe at about 10 past 5 in the morning and calls at a random arrangement of stops via Earlestown and Warrington BQ.
If you’re going to run an infrequent service, at least run them at a time that people could make use of.
One that gets in Manchester between 7.30 and 8.30 and one that leaves Manchester between 1700 and 1800.