PDF is branded – there’s a brand impression for you.
For me, though, I tend to make an HTML version of important PDF files. Sure – allow them the download still – but do the best I can to provide the same thing as an “in-browser” experience. Google will tend to favor the HTML version in most cases – especially if (near the beginning) you’re offering up the PDF version as an alternative.
Still, for me – from a digital marketing perspective more than a pure SEO perspective – brand the hell out of your PDF downloads. Those things get handed and/or printed out for proposals, training sessions, and sorts of things.
And, of those PDF files get posted elsewhere, even though the links in them are treated as nofollow – there is almost certainly stuff going on that helps establish your brand entity and its relationship to the things within the document(s).