Destructix, if I interpret you correctly you think Limerick Junction to Waterford merits retention while Ballybrophy to Limerick should be closed. You suggest that despite Irish Rail, usage on the Waterford line is better than on the Ballybrophy line.
While the overall situation of the Limerick Junction to Waterford line is better than the Ballybrophy line this arises, in part, from the fact that Irish Rail were dragged kicking and screaming into improving the schedules and connections on the line. Nonetheless the sparse service, the lack of through trains between Limerick and Waterford, the minimal commuter options, the lack of a weekend service, low speed, lack of marketing and low quality rolling stock all contribute to underutilisation of an asset on which significant public funds have been spent on track renewal, bridge renewal, level crossing elimination and fencing.
Most of the above factors apply to the Ballybrophy/Limerick line where again any initiatives to improve the service have been forced on Irish Rail. I have no doubt that Ballybrophy to Limerick has the potential to be a successful Intercity route as well as a source of commuter traffic to both Limerick and Dublin. Unfortunately even if there was a will to develope to the line, there isn't the money at present to reverse almost 40 years of neglect and dis-interest and to sort out the idiotic track layout at Ballybrophy and the operating overhead associated with the disproportionally large quantity of level crossings between Birdhill and Killonan.