AlexderFranke: A few observations. I would agree with much of what you have to say, but there are some reservations.
First, forget about re-opening Athlone-Mullingar as a solution to congestion between Athlone and Portarlington. Doubling some or all of the latter would better (and more directly) address the problem. Remember that the Mullingar to Dublin line is already pretty busy and there are really big problems over the last few miles into Connolly.
I would put serious improvement to Waterford-Clonmel-Limerick and to Limerick-Nenagh-Roscrea-Ballybrophy over any new/reopened lines north of Athenry (or maybe Tuam). Also, forget about Rosslare-Waterford. I say this because some lines have no big urban settlements en-route.
Think seriously about how the railways can take advantage of higher carbon taxes, which should favour relatively fuel-efficient modes or transport, especially if you throw electrification into the mix.
Finally, Germany and most European countries make a sharp price distinction between Intercity (only reserved seats and often high fares) and regional/local/commuter services (much lower fares and no reservations). In Ireland we have Intercity trains effectively doing a lot of commuter work. Maybe this is inevitable in such a small system. (but if the system were to get much busier in a post-carbon era? ….)