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ePub allows for "richer" formatting. You can, for example, have things like "drop caps", pictures with text that "flows" around them, or embedded fonts, none of which Mobi supports.
The primary benefit though is simply that ePub is an open standard, while Mobipocket is "owned" by Amazon. That means that there's a much wider range of tools available to create ePub books, and stores from which to buy them.
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