I think that a codex is absolutely the best format for something that you have to be able to flip through. Certainly an improvement on the scroll. (Though if the info is on line you can have multiple open tabs/windows which does nearly the same thing).
But for reading most fiction, where the point is to start at the beginning and go on the the end, an ebook is perfectly satisfactory. Of course, with the ebook, you can book mark favorite passages to go back to with reasonable efficiency, and if it's indexed it is possible to find specific information. But I agree that 'flipping through' just to find a 'good bit' doesn't work well.
As to a menu choice for ToC. . .there is currently a menu choice for 'go to' and one of the options IS ToC if the book has one. Of course, as you note, not all do.
