I agree about too long TOC being a pain. My first book (>140k words) was 21 chapters and split into two parts. On the print edition that sits nicely on 1 page, but on the e-book edition I could see potential issues: both the length and the two-level aspect. The two levels worked on my e-reader but I didn't like it - especially since the prologue comes before Part 1, it just didn't look right to me.
So when I created the epub I made sure the parts were not part of the ncx - resulting in a flat index. Yes it skips the part selection when using the e-reader TOC feature, but I thought that was more practical to use. (The parts remain visible on the TOC page at the start of the book, and as separator "pages" in the content.) I will be curious to see if I get any feedback about that particular aspect.
Chapter titles are interesting too. As a reader I don't really have much of an opinion either way - sometimes they're sort of neat/cute, but I don't really care if they're not there. But when I started writing this project I decided to use chapter titles, mostly because the chapters in my first book seemed to come by their titles fairly naturally - most were written with the title already in place. My problems really came with the second book (and since it's part of the same series I wanted to retain the same style) where I had to work a bit harder to get titles I was happy with (it's amazing how much work you can end up putting into a single word). I've yet to find out how it's going to come out with the third.
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