One that's been irritating me lately: Allow even smaller paragraphs to split over multiple pages in Kobo epubs, rather than starting a new page. It leaves far too much whitespace and causes extraneous page turns. (especially when you have paragraphs that are just slightly too large for the page, the only case where they naturally split, and you end up with only a line or two on the next page)
And, on the publishing side, it'd be nice to not have books broken up into one chapter per file (since it slows things down a LOT at chapter transition). :/
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