From the point of atmospheric science, NCL has certain natural advantages in dealing with self-described meteorological data formats, but R is improving significantly.
Unformated Binary
I have to say both NCL and R are not as good at reading/writing binary files as Fotran, though technically they are able to do the job.
Self-decribed Binary
NCL uses a single function addfile to handle all format (netCDF, HDF, GRIB, CCM, shapefile), while R requires additional packages.