Right now, ebooks are a byproduct of paper books; the distribution and publishing process is identical, while the reading experience differs only slightly. The current crop of ebooks takes advantage of the digital format in as much as they permit you to carry more of them around than you could before; but other elements of the medium — “hyper” part of hypertext — are noticeably absent.
Many developers are sticking closely to a paper metaphor in apps used to read these books. The paper metaphor can be done away with. Books that play video and show passages others are highlighting don’t need “pages” with a fancy curl animation. Scrolling is a better method on a touch-based device, but probably isn’t the best answer. It will be interesting to see what other conventions are explored as devices and the format mature.