I would definitely prefer a single PDF to the current multiple file approach. It doesn't seem as though it would be that hard to do top tier bookmarks for each of the current sections, then do sub-sections under that, such as for the various chapters and locations in the main adventure. I would find that approach a lot more useful for me personally, although I usually do my PDF browsing on fairly capable computers and never on my PDA, so I don't know how changing it would affect those users with lower-end machines. An option for one file would be nice, though, even if the decision is to keep the default method the way it currently is.
I do realize the PDF is a 'freebie' for subscribers, but it did play at least some part in my decision to become a subscriber, so I don't consider it unimportant. And, as the first poster said, if I'd bought only the PDF version, I think I'd be a little underwhelmed. The production values are beautiful, but the features currently leave a little to be desired, and there's no way to change that with the PDF locked down as it is.
I do understand why the security features are as they are, but I do question the effectiveness of the lock down. It prevents customers from doing things they might legitimately wish to do with the files, such as combine them or add bookmarks, and I don't believe it does very much to thwart dedicated pirates. Nor do I think not releasing a PDF would do much to thwart them. Scanners are cheap, and OCR software's readily available. The final result probably wouldn't look quite as nice, but if Pathfinder proves to be popular, I believe copies will start showing up online, no matter what security measures are in place. I wish that weren't so, because I do want Paizo to continue to be successful and release new products, but I think they'll have to do so in spite of people who get their products without paying rather than because they've made such impossible.