You might try the implementation of the Olive Tree Bible software. I think you can get the KJV for free on the app store. It has some things I would like to see on a book reader.
-Highlighting, different colors all editable by name and color. LIst of highlighted passages. -Notes savable to evernote.
-Search function.
-Copy and paste.
-Bookmarks.
-Really nice implementation of footnotes, they pop up on the screen in front of the text when you click on the number. T
-The popup feature also available for other texts you might consult while reading, dictionaries, lexicons etc.
-Split screen view so you can compare texts or see notes or footnotes in the split screen.
I imagine it's a little easier to do with a Bible program because of the chapter, verse layout, but it's what all book readers should look like.
Reading on the iPad