The problem I've found with saving pdfs as eps files is that sometimes they don't change over correctly. If a font is protected or missing or damaged somehow in the pdf file, the type in the Illustrator eps will be wrong... words may break in the middle and overlap themselves. If there's a lot of small type, it can be hard to spot until after the job's been run. Although, I haven't done this since the CS version of Illustrator and Acrobat 6, so maybe they're more compatible now.
I have also noticed, at least in Quark 5 on the PC, that when I import a pdf, sometimes the font will completely change. It doesn't tell me that fonts are missing or anything, but it even looks wrong in the screen preview. If I bring the same pdf into ID2, I get a missing font message, but everything will output correctly, and looks correct on screen. Perhaps QXP6 has fixed that problem, but we haven't purchased it for PC yet.