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In addition to everything rashkae mentioned:
Kepubs support fast page flip, which is quite useful when looking for a page.
Kepubs support footnote previews.
Kepubs have epub3 support.
An alternative to the Calibre plugin is kepubify, which is quite a bit faster, works from the command line and scripts, can update series metadata without needing to manage your whole library (this feature can be used on its own too), supports syncing a dir with your kobo, and is standalone. Note that kepubify is not for you if you use calibre heavily or want to convert from formats other than epub, as I haven't finished the calibre plugin yet.
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