Say at some point you felt it would be a good idea to have your emphasised words no longer in italic but in red and roman, you'd be faced with the awkward moment of defining the <i> tag as roman in your stylesheet. No such problem with <em>.
Basically, if we want to design with italic we should be making print books, not ebooks. To regard an ebook as an e-equivalent of a print book is just a short period in history when we couldn't see too far ahead.
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