Given the usage of the stations, you'd probably stop every train at Mallow and Limerick Junction and then alternate the other stop between Thurles and Port Laoise. It may be desirable to stop one or two trains to connect with Mayo trains at Portarlington.
Other stops could be better served by Thurles-Cork and Thurles-Dublin stopping services or even a Cork-Dublin stopping service, which gets overtaken by the express train at some point and which allows connections to the express train at Thurles. Such services could increase the number of stops at places like Charleville, Templemore etc. and could facilitate services to stations that are planned to reopen (e.g. Blarney) or are long closed (e.g. Buttevant, Dundrum).
It's the way rail services work elsewhere.
Without the padding and with three stops, I see no reason why 2h 25m or 2h 30m shouldn't be possible. If you want to see the effect of padding, have a look at the following timetables between Cork and Mallow.
Somehow, Dublin-Cork InterCities take 6-13 minutes longer than commuter railcars; they mysteriously take between 31 and 38 minutes to do the same route with the same rolling stock and no stops with no obvious reason why one train is faster than another. Most tellingly of all, while it takes between 31 and 38 minutes to go downhill from Cork to Mallow, it takes 21 or 22 minutes to do the uphill journey in the opposite direction.
