Here's my summary of the issue, as of November 2014, that I've just posted to another discussion group where I've been discussing the topic of footnotes in EPUB books:
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Thank you everyone for your feedback. Apart from that received in this group, there have been some excellent, eye-opening follow-up posts to my own lengthy MobileRead post exploring the issue, a few of them penned by true EPUB professionals:
https://www.mobileread.com/forums/sho...62#post2972962
The consensus is clear: no
<aside> tags for now, and (sadly) not even the potentially highly useful
epub:type="noteref" and
epub:type="footnote" tags for now, either, although these might be – no matter how "non-standard" doing so would be – implemented inside our current EPUB 2 coding without any problems whatsoever. A simple search & replace operation, and you're done – each footnote and footnote mark would be instantly and unambiguously identified, so that popup (and other types of) footnotes could become reality
right now, instead of us waiting for some distant future of universal EPUB 3 acceptance.
So, it appears that Liz Castro's joy over the birth of popup footnotes in
that blog article from 2 years ago was premature and, to uninitiated readers of her article today, perhaps misleading. (It doesn't help that Ms. Castro is notoriously known to be Adobe-centric and Apple-centric.)
And so, for now, the wisest course of action seems to be to stick to the "low-key"/conservative/cautious/traditionalist, even if slightly unwieldy and unsophisticated, way of presenting footnotes as standard "back-and-forth" hyperlinks between the main text and the footnotes section, laid out as
endnotes (ideally at the end of each
chapter, rather than the end of the book, especially if there are many of them). Further, it might be wise to avoid superscripts for footnote marks, opting for something like this: [23] (in regular font-size) instead.