In making maps in R, the biggest point of pain for me has been reading in shapefiles. D3 has been far better for making maps because TopoJSON’s topological format for representing geometries is so much better than the format of shapefiles. Bob Rudis’s post “Overcoming D3 Cartographic Envy With R + ggplot” taught me that the most recent version of GDAL/OGR can read in TopoJSON, and thus that the R package rgdal can as well. This will make mapping in R much easier.
I've recently migrated this blog, and the older posts might not yet be satisfactorily cleaned up. Apologies for the temporary mess.