I think it makes more sense to keep the Liverpools and Manchesters as the slower services. A significant part of the market from those cities is tourism, and Shotton and Flint aside, pretty much all stations along the coast are tourist destinations in some form. Holyhead for the ferry is a minority destination - most people wanting to go to Ireland as foot passengers fly, and in any case neither service will go to Holyhead.
My ideal pre-HS2* would be:
1tph London-Holyhead (Stafford, Crewe, Chester, Flint, Prestatyn, Rhyl, Colwyn Bay, Llandudno Jn, possibly Conwy**, Bangor, Holyhead) - more or less as now but hourly
1tph wherever-Shrewsbury-<some stops>-Chester, Shotton, Flint, Prestatyn, Rhyl, Colywn Bay, Llandudno Jn, Bangor, Llanfairpwll, (request: Ty Croes, Valley, Bodorgan), Holyhead
1tph Manchester Airport-Manchester Picc-Oxford Road-Warrington BQ-Frodsham-Runcorn E-Chester-all stations to Bangor with Llanfairfechan/Penmaenmawr on request.
1tph Liverpool Lime St-Runcorn-Chester-all stations to Llandudno
1tph Llandudno-Junction-Llandudno shuttle before the Liverpool heads back
Whatever the Conwy Valley gets (different thread).
Chester-Crewe shuttle in the opposite half hour to the Avanti
So looking at the stations that would be the following served by all trains: Chester, Flint, Prestatyn, Rhyl, Colywyn Bay, Llandudno Junction
Llanfairpwll, Ty Croes, Valley, Bodorgan, Holyhead: Only served by the Holyhead
Llandudno: Liverpool plus a shuttle to the Junction in the opposite half hour
Llanfairfechan/Penmaenmawr: only served by the Manchester
Conwy: served by the London ideally, plus the Manchester and the Holyhead
Shotton: served by the Holyhead, the Liverpool and the Manchester (due to its connectional value)
Abergele: served by the Liverpool and Manchester (because it's a beach day out that might be desirable from either)
I think that's it. Though there's the option to chuck things into the mix like a "Y Sherpa'r Eryri***" or something as a DalesRail-a-like from Liverpool/Manchester onto the Conwy Valley with connecting bus services to Pen y Pass and the likes which I believe is being actively considered by TfW, but this could be chucked into the pattern above as a portion.
* Post HS2 it is worth giving consideration to terminating the service from Cardiff etc at Chester, and replacing it with a service from Holyhead to Birmingham International via Stafford as used to run, or somehow portion working both. It can't be pathed now, though. If this was implemented the shuttle would be removed.
** If there was a good connection in both directions at LLJ then this call would not be needed, but as it's a holiday destination and people holiday in North Wales by train from London (though not as many as do from Liverpool/Manchester) then this call may be worthwhile.
*** "The Snowdonia Sherpa", to differentiate itself from "Sherpa'r Wyddfa", the bus service.