Actually, playing around with HTML export vs. saving as PDF on my own, it looks like they're quite similar. Here are a few observations:
1) HTML export seems to always display the Note field, even if the Notes were collapsed in your OmniFocus window. Save as PDF, on the other hand, only displays the notes if those fields are being displayed in the OF window.
2) Save as PDF preserves action color-coding, where as HTML export shows all items in black.
3) Flags appear orange in HTML but black in PDFs.
4) Headers (such as context groupings) are more prominent in HTML with a gray background. In PDFs, only the text is printed.
5) PDFs display checkboxes next to the actions, HTML does not.
6) In my test, using my errands and shopping contexts, the HTML file came out as 12 KB while the PDF was 36 KB. Not a big deal for small lists, but might be a factor when doing your whole database.
7) Personally, I find the PDF slightly easier to read - something to do with spacing and color-coding, I think. Or maybe it has to do with the checkboxes acting like bullet points.