One thing that I don't like about all the iBooks (including all the Bible apps) I've used is that they don't provide any visual consistency when you return to a specific page.
As someone who is highly visual, it helps orient me to have fixed pages. I'd like to suggest a change to make the content of each page consistent. For example, if I search for "Ephesians 3:5" it should take me to a page and that verse should always be at the same position on that page no matter if I had searched for it, or if I was reading Ephesians from start-to-finish.
To accomplish this would be fairly simple, I think. Just render each book with the start of the book at the top of a page. Then, assuming I don't change my font settings, every page thereafter would always be the same.
This would be immensely helpful to me, especially for memorization as the visual cues on a page aid my memory a lot. For that reason, I usually use a physical Bible for memory.