I use the Kindle app on my iPad and have also seen the OliveTree blog post with the screen shots of their iPad app... As a result, it seems like it wouldn't be too much to ask to have a few additional appearance options for Logos on the iPhone/iPad: sepia and black background, bookmarking, and font size adjustment on-page instead of on a separate screen.
I would most like the sepia and black options for reading in bed and reading more comfortably in general (I find myself using sepia with the Kindle all the time).