Inniskeen, my view would be that given the current state of the N24, Limerick Junction-Waterford needs fairly minor upgrades and operational adjustments (such as Sunday service) to not only compete with the bus alternative but to become the no-brainer choice. How much more money will be spent on Nenagh track and structures just to make up the time difference while still leaving Killonan-Nenagh with comparatively high staff costs?
If Limerick Junction-Waterford is reduced to a siding then it will still see some movements to and from Limerick Depot as 2800 home base and wagon maintenance centre. If Nenagh Branch closed the likely impact would be much smaller on non-revenue traffic, and the paucity of use during the Lisduff shutdown indicates to me that it doesn't add much from a redundancy point of view.
Measured in passenger trips I suspect a much higher return for the Limerick area of the track and tamping works would have been a refit to Limerick yard track and upgrading the track toward the Junction to *at least* 70mph all the way but preferably more. That would improve not just Limerick-Dublin and Limerick-Cork but Limerick-Waterford timings too. Instead when you punch in Limerick-Portlaoise to the journey planner not a single Ballybrophy route shows because the services via the Junction routinely overtake.
The Nenagh branch is the wounded, sick old antelope. Let the lions have it so the rest have a chance of getting away.