Electrification to Holyhead from Crewe as West Coast infill. Followed by Newport - Chester as the North South Link.
Not so sure about Newport - Chester as with the North Wales coast line electrified that would be the only route for 175s (since I think their depot is at Chester), once they are life expired though put the wires up ASAP.
As for new lines I would suggest Carmathen Aberystwyth, Afon Wen Bangor to give a Welsh WCML▸ . It wouldn't have to be full high speed say 100 mph in parts so straightening out some curves on the existing alingments would help
I'm not sure that's such a good north-south line myself, but do think Carmarthen - Aberaeron should be re-opened to reconnect Cereidigion (and later do Lampeter to Aberystwyth too). The north-south route I proposed would be:
- Cardiff - Merthyr - Electrified (along with Vale of Glamorgan line) linespeed upgrades (100mph where possible, for use by valley lines Electrostars)
- Merthyr - Brecon - Continuation of electrified Merthyr line of Valley Lines on a completely new route, much straighter route than the orriginal, with 100mph most of the way[/i]
- Brecon - Near Newtown - (probablly mostly 90mph and no wires) with new alignment between Rhayader and Llanidloes
- Near Newtown - Porthmadog - 90mph where possible on Cambrian mainline
- Porthmadog - Caernarfon - not using Afon Wen, as suggested here
- Caernarfon - Bangor - electrified during re-opening
As you say, these, and many other lines which I think should re-open, could use some new tunnels and gentler curves to increase linespeeds though I would say 90mph rather than 100, as that's what a class 158 'Alphaline' can do and they are probablly my favoriate DMU▸ (unless you count INTERCITY 125s as DMUs).