PDFs are great for
reading, but nothing else. If you want to
do something with the text, then plain text or some derived format is better. I would include searching as "doing something". PDF viewers can search, but it's always more painful than searching plain text, and I would say if you're using search to simply locate your subject in the file, then the file author has failed to provide a sufficient TOC/index.
To me, the case in point is the PDF documentation of LaTeX packages. The PDF files are great as a demonstration of what the package does, but they are awful for learning how to do it in your own documents. I am writing LaTeX in plain text, in an editor. I want the package documentation in plain text, in my editor. I sure as hell do not want to fire up a separate PDF viewer and then start flicking through pages, just to discover the correct package option incantations.
I love PDFs, but I only love them as a prose reading experience: open the file, start at the top, read until the end. When I make PDFs for other people to consume, I usually make three different layouts: print, screen, and tablet/mobile. Thanks to LaTeX, that's easy to do.