Great article.
Supporing embedded fonts is probably the top desideratum, but the others are important too, and not just for the iPad, but for ebook readers generally.
There is of course, still the option of converting the ebook to a properly sized PDF, and then even the iPad will display it right, using something like pdfLaTeX or Prince XML which can do hyphenation and widow/orphan control, kerning, ligatures, etc.
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