Ideally, ePub would be "reflowable HTML plus baked-in things you would obviously want in a book made dead simple for author-editor-publisher workflows that will never involve a programmer in a million years". Proper footnotes that appear on the same page as the thing they're footnoting, for example.

In practice though this is still a shitshow even in ePub 3, 99% of publisher just ship a pile of endnotes, and consequently certain authors like Terry Pratchett are a god-awful experience in ebook format. Jumping back and forth every 30 seconds sucks.

There are work-around that can be done with JS or certain reader-specific markup you can use for iBooks to at least get pop up footnotes, but most publishing houses don't have the technical knowhow or desire to invest that much time in doing the right thing. There needs to be dedicated markup and a better standard for how readers should treat its display whenever possible.

A real failure of the standardization committee, and it will likely only get worse with a group that cares even less about books specifically. The standard continues to be driven by people more interested in gee-whiz features than solving longstanding problems in replicating table-stakes features of print.