I would have trains running Birkenhead North - Wrexham Central every 30 minutes during the daytime, more or less timed to pass each other more or less at Shotton.
The ex Chester & Holyhead (north Wales Coast) downstairs would have both the Manchester Pic - Bangor (Gwynedd)/Caernarfon via Warrington Bank Quay and the Liverpool Lime Street - Llandudno via Halton Curve (60 minutes frequency for each, providing a combined frequency of every 30 minutes along the common section between Frodsham and Llandudno Junction calling all stations along this section) calling 15 minutes either side of the Borderlands trains upstairs and timetabled to more or less pass each other downstairs.
This would enable an exchange of passengers arriving and departing in the other three directions with no more than a 15 minute wait to do the interchange, and would go some way to help encourage people to leave cars at home and use public transport, as a 5/55 minute interchange is not very friendly at all.