I hope Dublin-Limerick passengers the appreciate the haul up and over the running lines from the new platform to the Limerick connection, which will replace the present easy cross-platform connection. A couple of wheelchair-confined passengers will ensure that the interval between arrival of the down Cork and departure of the connection to Limerick will take much longer than at present.
As for Waterford, any new station will not be as close to the bridge so that's one inconvenience. Given that passenger trains will have to run along the present through road (deemed unsafe since the rockfall), why not spend some money on additional rockfall protection and leave the station where it is? Use the savings to automate a few more level crossings and save on operational costs.
Irish Rail projects may be well-engineered, but are often hopelessly inappropriate.