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As pilotbob said, epub is essentially a base format which is intended to port to a variety of independent devices. The problem is, much like CSS when it was fresh, support is a bit haphazard in places.
I think a more important question is: How can developers make better epub-reading programs? iBooks looks to be pretty run-of-the-mill so far, and if Apple doesn't reject them, superior independent epub readers could be developed.
If you are an epub file creator, just carry on as usual, I'd suspect.
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