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One of the issues is, that if you do footnotes as they should be in ePUB3, they will not work in ePUB2 at all. So you either need to do them double or accept that with a normal e-ink reader there will not be any footnotes. The choice is easy then.
There are some benefits to ePUB3, but most are related to CSS3 and not the real ePUB3 specs
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