I wish epub was more common for papers. I have no idea if there's any real difficulties with that, or just not enough demand.
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Is there an epub reader that can format text approximately as usably and beautifully as pdf? What I've seen makes it noticeably harder to read longer texts, though I haven't looked around much.
epub also lacks annotation, or at least annotation that will be readable across platforms and time.
Not really what you want researchers to waste their time doing.
But you can use any of the numerous html->epub packagers yourself.