The first problem is organizational. You have an epub bookshelf and a pdf bookshelf. I would prefer a unified bookshelf. It would make things easier to find when there are large numbers of documents and one doesn’t remember what the document type is.

The more important problem is that pdf support doesn’t have a way to crop margins that I can see. You can unpinch to zoom in but that’s a bit fiddly and to make matters worse, it zooms back to full page view when you change pages. I was hoping I could use ibooks as the One True ebook reader but it’s not there yet.