Producing the current book I'm working on as EPUB 3 (especially as
only EPUB 3) makes no sense – EPUB 3 does not have wide enough support for now. So, the new
<aside> tags are out of the question for me.
However, I wish we could simply include the other tags Liz Castro talks about,
epub:type="noteref" and
epub:type="footnote" in our EPUB 2 books and their traditional hyperlinks coding. I know they don't belong in EPUB 2, but they would make every footnote and footnote mark instantly and clearly identifiable, so that no more guessing and heuristics on the part of Moon+ Reader, Kindle Paperwhite et al. would be necessary, and popup footnotes might become reality even in EPUB 2 books.
I'm afraid, though, that it's too early for
epub:type="noteref" and
epub:type="footnote", too, in terms of general acceptance. Sigh.
Liz Castro sounded ecstatic about them back in May 2012, but it doesn't look like they've gained any sort of traction to speak of since then.