1. These endnotes, which are bog-standard ones, could be better: A couple pages of footnotes from Hacker and Pierson's _American Amnesia_ The only waypoints they leave for the reader are chapter headings. So if I’m in the middle of reading chapter 5, for instance, I first have to figure out which chapter I’m in (not always easy — in many books this requires you to flip back a good many pages); then I need to flip to the start of the endnotes for that chapter; then I need to flip forward to the endnote that I actually want to look up.
    The correct way to do endnotes in printed books is to have “Footnotes to pages A-B” at the top of each page of footnotes. It’s much faster to navigate.
  2. Kindle books, and particularly Kindle books’ footnotes, were clearly designed first in print and then hastily ported over to e-books. The footnotes to Robert Gordon’s book, for instance, just say “Smith (1998)”. It would be mildly annoying to look up Smith (1998) in a paper book; in a Kindle book, it’s annoying enough that no one is going to do it. First, getting to the bibliography is often nontrivial, and then getting within the bibliography to the particular work you’re looking for involves (as it did with Gordon’s book) endless swiping. Then getting back to where you were reading is tedious.
    The correct thing to do here is obvious, once you acknowledge that the cost of a marginal character in a Kindle book is essentially zero: don’t even bother with the classic “footnote pointing to a bibliography” citation form. For that matter, don’t bother with ‘ibid.’ or any of the other holdovers from a time when you needed to save on space. Rather than “Smith (1998)”, include the full cite every time: “Smith, Robert A. Blah blah blah blah. Page 93”. If you absolutely must use the old citation method, can’t you at least provide a hyperlink from “Smith (1998)” to the exact spot in the bibliography? But there’s really no reason to accept old formats for new media. I expect the only reason the old style persists is that publishing workflows can’t produce separate e-books and physical books. But that needs to change; the media are different.

I acknowledge that I’m one of very few people who even bother with the footnotes and endnotes, so this isn’t exactly a market that publishers are going to throw their best people at satisfying. Still, there are right ways to do notes, and there are wrong ways, and publishers do it wrong much more often than they do it right.