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EPUB3 is a complete waste of space, on account of if you create an EPUB2 it will already work everywhere. The only reason to start with an EPUB3 as the comments suggest is if you are actually trying to produce an EPUB3 ebook.
Which is extra work for no net gain, although people are more than welcome to waste their efforts doing so anyway. They have free will.
Unless you are creating an ebook that actually uses EPUB3 features, in which case you won't have ever been asking the question "which one should I use" in the first place.
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