Make the text display page oriented, like a book (iBook and Stanza do this).
Rather than putting an entire chapter into the text object, display only one page of text, so that there is no scroll bar. Spacebar or Page Down will display the next page, Shift-Spacebar or Page Up will display the previous page. Allow swiping to change the page rather than change the chapter. Perhaps swipe up or swipe down can change the chapter.
Currently the way things are, the last line of visible text might be only partially shown. When you display an entire page, don't allow for partially displayed lines in the last line of visible text.
Tofu is interesting as a proof-of-concept, but drop one of our Take Control PDFs on it to see how troublesome this kind of thing is. No graphics, not much in the way of font support, major issues with line endings (that's due to relying on PDF), and no support for links (again, that's a PDF thing, but it could be a problem in EPUB too, in terms of being able to identify the destination).
George Jarrett commented
Check out Tofu to see it done well: http://amarsagoo.info/tofu/
We're looking into how hard it is to do this - the initial goal was to provide an app that worked the way Mac users would expect, which means a scrolling approach like nearly every other text-based Mac app out there. Remember, EPUB is a reflowable format, so a page is an entirely arbitrary concept with EPUB - no two people will ever see the same page, based on window size, font choice, and font size. Plus, on the Mac, scrolling is one of those things that's very easy and built into many controllers via scroll wheels, scroll balls, and more.
My hope is that we'll be able to provide a two-up view that will offer a left-right page flipping option.
The problem with the last line is frustrating - WebKit isn't giving us finely grained control over how the text is displayed.