Yeah, that's part of what I have noticed. I keep hoping to see the new pdf engine in Calibre as released and working well. Sadly, a lot of my eBooks are magazines with some heavy graphic content. If they were mostly text, then the conversion would be a much easier task. I do wonder though, even if I were to not convert them but clean them up, optimize them somehow, in order to get the right height/width, i.e. resolution, with decently clear images, that would display better on a recent iPad, could that work better? If so, any idea as to how to go about doing that?
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