Originally Posted by JSWolf
a linked ToC internally which is not wanted and not needed.
Just my two cents: I would want both. The internal TOC is a tradition that makes book a book (as well as the title page, chapter division, preface, introduction, etc.). Without it, epub is just some text with navigation. I'll use the external one for convenience but the internal TOC is a must.
I am not a Luddite (see the list of my devices) and always on the lookout how the books can be improved. Even with the change from paper to electronic screen, a book should remain a book (not a twit, email, blog, etc.). It has a long history. It can gain new characteristics (video illustrations, etc.), yet it should be still recognizable.
On another note. With all the talk of the superiority of epub, it does not have the dictionary or internal index support. I am not talking about one default dictionary, I am talking about a format that I can use. Come on, Mobipocket had it years ago. You can do fancy stuff with it (you can insert paradigm wordforms for a headword!)
I also have not seen a good, fast text search implementation (comparable to what Kindle offers). The Nook C only searches forward. The last may be not the format's fault but still.
You can put a gigabyte of structured text into a mobipocket on the Kindle (has been done with Wikipedia and such) and the search, indexing, navigation, etc. works great. Large epubs are slow (even if you do all the tricks). So, for a medium-sized novel, epub is great but for a large reference work it is nowhere near Mobipocket on the Kindle. I would love to see epub develop beyond eye-candy.