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It's going to depend on how the PDF was made. The problems you're seeing aren't with the conversion program or the new filetype; they're formatting issues from the original PDF that aren't obvious.
For example: pretty much anything that converts from PDF will keep the original page breaks as paragraph breaks. These would have to be removed manually, or with some kind of script that knows how to detect which of them are real paragraph breaks, like the end of a chapter.
Untagged PDFs will often put a paragraph break after every line of text. (Tags can be added with Acrobat Professional; I'm not sure what else will add them, or if other programs that convert the file will auto-tag as they go.)
One of the common complaints about PDFs is that you can't know how well it'll convert or even edit, unless you know what program made it and what settings were used. PDFs made directly from Word documents tend to convert back to other formats fairly easily. PDFs made from InDesign, which a lot of professional ones are, are more touchy. PDFs made from other kinds of publishing software are often nightmarish to convert.
The best advice is probably to figure out what kind of errors you're consistently getting, and see if someone's written a program or script to address those problems.
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