> Part of the problem is that as datasets get bigger, it's rarely sustainable to put a lot of care into each and every version of a plot, but automating creation of figures is really hard.

That's actually a good reason to learn R and the ggplot2 package. Whenever I write a paper, what I do is that I make a quick shell script that invokes Rscript, with a simple R program that takes a CSV file and outputs a PDF file of the plot, which can be automatically loaded in LaTeX.

Whenever the data changes, it's just a matter of updating the CSV file and running the script that rebuilds the figures and the LaTeX document. As an added bonus, it makes keeping the data with the paper easy, since they're part of the same source control repository.