Have you tried both GoodReader and neu.Annotate? I seem to remember the neu.Annotate developer talking about a feature that resembles what you are missing.
Plus, remember that PDF isn't really a suitable format for e-books.
It's an anomaly, when nothing more suitable is available. I try to avoid PDFs whenever I can. On the other hand, they are suitable especially for older, photographed books, because that way I can avoid all the inaccuracies and modernizations frequently introduced whenever an old book is converted into EPUB or Amazon formats.