FlashPaper files are smaller than PDF files due to compression. If you compress both the pdf & the flash paper with zip, they end up about the same size. This is because swf's have built in compression while pdf's don't seem to.
Flash Player is slower than Adobe Reader especially when you make the window large, and are trying to scroll, you get a very sluggish interface (as compared to any normal application).
Dave Wraight compares Macromedia FlashPaper with Adobe PDF and feels that FlashPaper has a lot of potential to provide source content in a form that is useful inside other Macromedia technologies (Director, ShockWave, AuthorWare) and also in common web standards such as HTML.
However its future usefulness as a means to sharing content may be limited by either the underlying document format or the viewing technology.
Adobe recently acquired Macromedia and their PDF standard is already facing the heat from Microsoft's Metro which is being called by some as a potential "Adobe Killer".
See this PDF presentation on Web Standards: Redesigning Sydney Morning Herald