GoodReader, iAnnotate and PDF Expert are all really good apps for iPad designed specifically for PDFs. Like others, I think it's better to have a designated iPad app and a designated epub app, and get the best of both worlds, rather than attempting to mix the two.
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Originally Posted by democrite
PDF support would be great. After years of trying more or less all the major apps, I'm not that happy with any of them. If someday you get around to it, please consider:
- Sort by author and title, I don't know of any PDF app that shows the metadata instead of file name.
- scrollbar - displays document section just like Marvin and iBooks does with ePubs. not a single app yet I've seen.
- Dropbox sync - All apps pretty much requiring syncing a folder. GoodReader lets you sync per document, though you have choose it and make two choices (I believe) after selecting it on on Dropbox. Marvin's Dropbox search would be helpful for those of us that have hundreds of thousands of PDF eBooks.
- vertical scroll - hardly any of them do it yet it's the default view in Preview.
- annotations, could be added later
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Have you considered something like Bookends, Papers or Sente? They provide proper metadata fields and lots of organisation functions. Bookends has vertical scrolling (the others might have it, too, I just can't remember). All have annotation features, but not as sophisticated as iAnnotate, GoodReader of PDF Expert.