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.
Because what makes epub a format on top of html is just that someone QA'ed it and wrote the html/css with it in mind. Especially considering things like diagrams and tables.
Not really what you want researchers to waste their time doing.
But you can use any of the numerous html->epub packagers yourself.
epub is html, under the hood
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.