hadley, I couldn't pass up an opportunity to say thank you for ggplot2 and plyr. Both have made R infinitely more useful to me and have been used thousands of times by me over the past 3 years.
It is certainly a pollution of code -- a necessity to convert a good, efficient data structure which base graphics can plot into some specific form will always seem redundant from a programming point of view (and I was replying to a programmer).
Obviously the situation is opposite when one considers, let's say, "analysts", i.e. people that expect to be able to completely ignore the form of the data and focus purely on the content -- for them your stack of tools is a pure gold, even with its trade-offs.
I'd love to see an example of that - I agree that you might have to do some data transformation to use ggplot2, but I think the net effect is still fewer lines of code than with base graphics (except for v. simple graphics).
Some clarification about what you mean regarding efficiency would be useful - do you prefer arrays?
Boxplots from a list, matplot of a matrix, all the cool default plot methods for various complex objects like clusterings, trees, models...
Maybe I'm alone in that, but I believe the power of R lies in its resilience and the fact that it allows me to write code that is equally obvious in what it does as how it does. The philosophies of one-true-data-structure and natural-language-like expressions doesn't play well with it, though I admit they are very useful for people accustomed to a declarative programming.
