Merseyrail may operate a more efficient service than Northern but their Customer Approach is really just as poor.
The current management do like to run fast, turn short and stuff like that. The old approach, used fairly successfully for many years, was just to "step up" - as once a train got to 15 minutes late it was effectively the next one anyway, so you'd just cancel the one stuck in the middle. Historically Merseyrail never, ever skip-stopped (except for something like a station closed due to a fatality) and very, very rarely turned short - I think I experienced it once ever, and between 1979 (though I was a bit young at 0 to appreciate it!) and 2001 I mostly used it at least weekly in some form.
One issue might well be slower running and additional stations tightening the diagrams and taking out recovery time. Units used to lay over at Ormskirk for about 13 minutes (they would pass very near Ormskirk station itself), then at privatisation a unit was lopped out of the Ormskirk line circuit and this shortened to about 7 minutes, and has progressively become shorter as running times have increased from their original 28 minutes from Liverpool Central to Ormskirk to the present 34.
This has been caused by a number of changes - the first big change was hustle alarms, which added about 2 minutes in 1998 (prior to those the doors would be opening as the train stopped and closing about 10-15 seconds later), then we had staff being banned from keeping their door open while the train was moving adding a minute or so, then finally Maghull North adding to it again.
There was also a reduction in punctuality when crew changes started happening mid-run at Kirkdale - this didn't happen until about 1998. This probably also added a minute or so.
Hopefully the Stadler units can lop a bit back off with faster acceleration and door operation.