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Hmm, just a thought, but epub is essentially xhtml, right? Maybe I'm influenced by how BD does things, but I think that having the internal format represent the semantic structure of a book would be important, and I don't think xhtml covers the semantic space adequately. Or are there ways to denote poems, epigraphs, citations, etc. semantically in xhtml? If not, the internal format should probably be closer to something like FB2, except perhaps richer.
Both file input and output should be done via format-specific plug-ins, so it is possible to add new formats and change existing ones without having to change the whole application.
Make it cross-platform. If C++/QT is absolutely your thing, knock yourself out, but like kovidgoyal, I suggest taking a look at Python/QT instead.
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