There are many pitfalls to be avoided when working in Illustrator. Beyond it being buggy and a hog I find it’s not a great tool for working on any press-ready artwork. [Disclosure: InDesign fanboy here].

Firstly, as Aandi notes, avoid flattening artwork (ie printing to PostScript or saving as PDF 1.3 or under) – as that causes many transparency effects, including drop-shadows, to be converted into raster art.

If you must export flattened artwork don’t forget to set the “Document Raster Effects Settings” (under Effect on the menu bar) to a suitable level. Unfortunately the default is 72dpi.

Also ensure that any important type or vector information is kept in a separate layer above “background” objects. The idea is to add a virtual layer of separation between type and effects. “In Front” and “Behind” is not enough – use layers. [The same applies for InDesign.]

Again Aandi is spot on: the “Save PDF with editing capability” feature can cause massive file sizes; the difference with the PDF of the cover of the magazine I work on: a few hundred MB or just a few MB!

Another thing try to remember to use “Save a Copy” or to otherwise be careful not to get your final delivery artwork confused with the working file. Its’s an inherent confusion in Illustrator: PDFs should really only be used as final artwork – not as a working file. I don’t like that at all. Particularly as I have to deal with these ambiguous duplicate files at work. Add an extra note to the file name or something. Please!

I said it here