There's a lot on this topic here including my own thoughts:
There is no difference in quality or reputation. The single biggest difference is the higher cost in RCSI.
The difference in travelling is also a factor. Bear in kind that UCD has lectures, labs and library all in one place in Belfield, with some time in the Mater. In RCSI you will be flitting between Sandyford, Stephen's Green, Beaumont in first year and Blanchardstown the second year. This adds time, expense and stress.
If money is a problem, like for me, the long summer holiday in UCD gives a chance to work, whereas the summer break in RCSI is very short. Added to the higher fees in RCSI, UCD is much the better option financially.
That said, if I was rich I would probably choose RCSI as I like the dedicated facility they have and the small class.