Yeah, nothing's ever perfect, is it?
I hold an optimistic belief that stuff like this will get better over time and fairly quickly IMO. This whole ebook thing is relatively new in terms of widespread popularity and general consumer acceptance and for sure, the current lack of certain de facto standards certainly doesn't help matters. But the ebook format war seem to be narrowing down from what little I know so I gotta believe that stuff will get more uniform and "better".
Do I get annoyed about the cover art stuff mentioned? Yes, I admit, on occasion, it does bother me a wee bit, though I do try not to let it ruin my enjoyment of actually reading the book, which really, is the whole point for me. Maps, artwork, forewords, pictures, etc...all important and I want that stuff in my ebooks for sure. An ebook must represent and contain exactly the contents that the physical version does IMO. [Well, as much as possible. I remember waaaaaay back where certain publishers would include value-added stuff like tear-off bookmarks with their pbooks - I still have a few laying around, most personally memorable being a few Clive Barker bookmarks that were included on some of his mass market paperbacks back in the day.]
Still, I don't find it so horrible to flip back using a couple of keystrokes/whatever. Meantime, I will simply be patient and wait [probably not too much longer] until epublishers get their act together once and for all. And as the smart folks mentioned, there may indeed be ways for people to roll-up there sleeves and fix stuff on their own if they are so inclined.