This should be a priority. The City line has always had an inferior service compared to Merseyrail proper. Apart from the Lime Street-Huyton stretch, which has a similar frequency, no station has anything approaching a Metro style service. The worst served are the intermediate stations on the main line from Edge Hill to LSP. When Merseytram was a possibility/pipe dream, one option was for trams to run over this stretch - on the slow lines of course - as far as a new on-street line from Parkway to John Lennon Airport. Incorporating this into Merseyrail would be a start; extending it to Speke (not just the airport, but to the huge but forgotten housing estate) would be common sense. The Council assured us that the money set aside, and no longer usable, for the tram scheme would be spent on improvements to Merseyrail; since then they have gone quiet.
The Bootle dock branch via Tue Brook has also been mentioned as a priority for re-opening: it would help to regenerate a very run-down area of the city. But again, the authorities have gone quiet.
Also, if Halton is now part of the Liverpool City Region, electrifying the CLC line at least as far as Widnes makes a lot of sense. How feasible would it be to divert WCML trains onto the current slow lines at Edge Hill, and run Manchester via Warrington trains as well as a Metro service to Widnes/Warrington, on what are now the fast lines to Parkway? It would avoid conflicting movements there, and if the Northern line were cut back to terminate at Parkway, there would be no junction problems at Hunts Cross either.