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My personal preference is epub. I find some of the quirks in the KEPUB renderer rather annoying, I don't need the title of the book at the top of the screen -- if I forget what book I'm reading, I have other problems to worry about. Using full screen mode to get around the header loses the information at the bottom of the screen again removing any advantage kepub has over epub in that area. My main use for hightlighting is for errors which I will edit and correct if they are too annoying.
What I do like about kepub is the zoomable graphics and the popup footnotes though relatively few of the books I read have much in the line of graphics or footnotes.
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