Mumbai-Goa via- Konkan gives you greenery journey, too many bridges and travel besides water, trains runs faster in this route
Pune-Goa via- shindwane ghats gives you hot journey means less greenery but not normal journey, you'll enjoy forts, desert type feel, eye feast views of small towns and villages from top of hills which feels like aerial view and many curvy routes, trains runs slowly in this route.
So if you are taking just RF trip then you travel like MAO-CSTM-PUNE-MRJ-MAO.