As a reader and an author wading into ebook publishing, there’s so much here I agree with.
I definitely know when I want to read a book physically rather than digitally and I’ll go out of my way to purchase it in that form. I also know there’s plenty of work out there I’m happy to read on my Kindle. I estimate my current paper vs. digital reading proportion is fifty-fifty. The debate over ebooks is presented as a binary choice when the reality is far more fluid.
As far as layout, I see ebooks today at the same stage as the early Web (circa 1995–1998) which had similar primitive options. Future improvements to ebook technology could yield similar improvements to layout and design, to the point that the publisher (or author!) can completely dictate the layout of a book right down to fonts, hyphenation, and spacing, while still offering ways for the reader to adjust it to their needs — I’m thinking of readers with vision issues.
My biggest gripe with the Kindle is how it opens a new book to the first page of the first chapter. Here Amazon screwed up. Show me the cover, then let me page through the front matter to the first page. This is the pleasure and ritual of reading a new book.