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The fundamental problem is that PDF was made to display a document exactly as it was created. This can be very important if you want to have something like a tax form or a job application print out exactly the same for each user. Epub, on the other hand, was made to reflow a document to fit whatever device the reader is using. This is important when you don't know in advance if your reader is going to have a wide-screen computer monitor or a mobile phone. So PDF tries very hard to keep exactly the original format, and epub tries very hard to make its format fit the device. You can see, I think, where the problem comes in.
Having sworn at more than a few PDFs in my time, I've come to the conclusion that the only way to survive, at least with the current state of the format, is to leave them as PDFs. If I try to convert them to other formats, they end up less useful than they were as PDFs. The conversion works fine for linear text (novels, for instance) and falls in the toilet when I try to use it for anything more complicated (auto repair manuals). So I've become resigned to pretty much sticking with PDFs. Also to swearing a lot.
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