I very much prefer kepubs:
* for all books the page looks better to me with a header and footer, whether the screen is 6" or 6.8" - but this is obviously subjective
* annotated books don't work well with epubs on kobo (they were okay with sony)
* the zoom possibilities for pictures are convenient
* the page number by chapter felt strange at first, but I wouldn't go back to the page number by books. This is especially true for complete works, or collections of short stories, and I jump page for each poem in poetry collections. If I want to know where I am in the whole book, I tap bottom centre to get the % top centre. Also I add the number of pages as a first line in the metadatas to have the information at hand.
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