It turns out that the setting under System Preferences » Appearances that sets the smallest font size to be aliased on-screen also influences PDF creation (which makes sense, as OS X renders everything on-screen as a PDF, I think).
So if you generate any (business) PDFs on your Mac make sure to go to that setting and set it to the lowest value (4 in times of writing). Otherwise all Fonts smaller than this setting will get a flag set so they don't anti-alias and look exceptionally bad.
The design decision why your personal choice of having ugly fonts in smaller font sizes should be hard baked into generated PDFs puzzles me. It strikes me simply as an over-eager implementation of a feature that makes the world a worse place.
Tested it on the latest Mountain Lion (10.8.2) - still applies.