I had a similar issue, and solved it using ImageMagics convert tool (http://www.imagemagick.org/script/index.php). That comes with linux and runs fine on Windows/Cygwin or OS X
convert -density 300 largeVectorFileFromR.pdf out.pdf
With -density 300 you control resolution (as DPI).
Downside: Text is rasterized as well, I understand that Michael does not want this.