Yes, some XML which is an expanded XHTML is probably the way to go (in fact Mobipocket is going that way albeit a bit crudely).
I use "HTML" and "PDF" only as names because they are the dominating formats for the two forms of ebooks. RTF would be an alternative term for HTML and TeX for PDF.
The main difference is that HTML recognizes that presentation of content can be done in different ways. PDF is unable to separate content and presentation.
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