1. it is extremely slow for numerics. slower than MATLAB. slower than python (with numpy). after talking to several stats people, it seems pretty much everyone ends up writing most of their code in C when using R. (in contrast, i didn't find this necessary in python or MATLAB for similar projects.)
2. its syntax is quite clunky. want to concatenate two strings? paste(string_a, string_b, sep=''). radford neal has a series of blog posts on R's design flaws: http://radfordneal.wordpress.com/2008/09/21/design-flaws-in-...
3. uninformative error reporting. by default, the stack trace isn't printed. even if it is, often the errors don't really tell you what went wrong.
i don't see any advantage to R over python. yield makes a nice replacement for the lazy evaluation of R.