The point of PDF makes this a difficult task. It's bad enough that they can be altered on readers in the first place as a PDF, by original intent and design, is supposed to represent a page that is for all intents and purposes set in stone. Its size, fonts, and overall layout are all designed to fit exactly on a particular size page. It is, in other words, a digital representation of a printable document with well defined pages.
ePubs and other ebook formats, on the other hand, are digital representations of words without actual pages.
PDF viewing will always be a pain if the screen you're viewing it on is smaller than the pages of the PDF itself. The best you can ask for is a good way to zoom and pan -- and for an e-ink device that functionality would drain the battery, not to mention the current refresh rates would make panning pretty jerky.
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