the main thing that R is lacking is the proper help and product documentation in comparison to Stata, Matlab, SAS and similar commercial software.
there's a package called OxMetrics, which has an interesting algebraic approach to model specification and scripting. it's hard to explain, but when you use it, it saves a lot of time, because it automates a typical model development life-cycle tasks and steps. I haven't seen a similar functionality in R.
UPDATE: if you speak with R enthusiasts they may say that R has all functionality you need through user supplied libraries. it's a truly open source platform, which comes under GNU license. the open source developers never complain for the lack of functionality, because when they do the standard answer is "why don't you write this module and contribute?" and this is the great attitude, which keeps the community engaged. however, this makes your question somewhat poorly defined, because as i noted, one could claim that any functionality is either already there in some form, or "why don't you write this yourself?"
Hence, maybe you should clarify a bit what do you mean by "lacking" functionality. e.g. I doubt that R has anything close to Mathematica's computer algebra capabilities, but I'm pretty sure someone somewhere might have written something to integrate it with REDUCE or other open-source package.