Come on, PDF isn't such a bad format. It can even reflow if it was saved as a tagged PDF. Of course, it all depends on the software that came installed on the e-reader and how it interprets it. If you bought your e-reader in 2007, don't expect to be able to read PDFs saved with more recent profiles. At least not without a firmware update (if there even is one available).
Some e-readers display PDF files using the PDF's built-in info, like page size, instead of stretching it either by width or height. This is the most idiotic issue I've ever heard of! If the PDF was built with a blueprint-like page size, the e-reader only displays a corner. Pff... Why isn't there an option to zoom in to a custom location for the entire book AND KEEP THAT ZOOM LEVEL? I think all e-readers should run Android. Then if one app doesn't read ePub 3 or PDF 10.1, just look for another one that does.
Anyway, what is this "PrimoPDF" you speak of? It's supposed to be free but it competes with NitroPDF? Yeah... Guess which one received better attention from the developers?
Adobe Acrobat is still PDF's granddaddy and always will be (they invented it). It integrates really well with Word 2010 - speaking of which, their (Filtered) HTML exporting doesn't preserve all the formatting. You'd think a big company like Microsoft would get it right. I think they did it intentionally to keep everyone from using something other than .doc and .docx. Even the .odt export is crippled.