I think intermediate-complexity graphics are where ggplot2 excels. If you want to do something like plot a bunch of small multiples, you'll have a much better t

I think intermediate-complexity graphics are where ggplot2 excels. If you want to do something like plot a bunch of small multiples, you'll have a much better time of it using facet_grid than wrangling with base graphics. Once your graph reaches a certain level of complexity, though, or requires a certain degree of customization, I think base graphics regain the edge. At that point I prefer the level of control you get by drawing things from scratch with points(), lines(), text(), etc.