I hope iBooks 3 will support more advanced ePub. Mention was made recently that the ePub protocol was being updated to handle math. Math and other technical symbols used in science are not well supported by any eReader protocol, leaving such books unavailable for eBooks.
Given the push for using tablets in schools, and the push for better STEM education, it's important that publishers be able to offer such eBooks. iBooksAuthor likewise will have to be upgraded to support also.