How well do you know your audience when you design a PDF? If you are sending it to 6 people, whom you work with every day, that should be an easy one to answer. If it's going to be downloaded from a website, by 5,000 strangers, that's a different story. One question which needs to be answered is if the audience expects to view spreads or pages. We see many big corporate PDFs which are designed as if they are still doing print projects, exclusively. If someone says, "What you need is found on page 72." does that mean the page number at the bottom of the page or is it the number you navigate to using Adobe Acrobat's tools? If your document's Arabic page numbers (1, 2, 3...) start a few pages into it, with the first few pages being lowercase roman numerals (i, ii, iii...), will it confuse the PDF audience? How about interactivity? If the audience browses the Table of Contents (TOC), do they expect to click on a line of text and have the document place that section of the PDF in front of them? Some of these answers could be in how the rest of the documents on their website work, now. If well-planned navigation is how the rest of their documents work, you know they'll be expecting you to have the same in the PDF that you are designing. However, as one executive once told us, "We print everything. Don't waste your time with interactivity." Yes, that made us sad to hear, but that's part of what knowing your audience is all about.
I prepare my PDFs for the lowest common denominator—in this scenario, someone without strong computer skills or knowledge of Adobe Reader.
I always set the initial view so that the file opens the way I want them to see it—if they have the skills to change it, great. I use hyperlinks in the TOC but also force the bookmarks window to open so that that is an option as they scroll away from the TOC. I always make sure my pdf numbering matches the document page numbering (front matter in lowercase roman, body using arabic numbering).