Here's one to add:
Do missing scene/section breaks within chapters irritate you?
That is my #1 pet peeve with all ebooks. In fiction, scene breaks are critical in changing the character POV, or voice. In nonfiction, it indicates a shift in topic or focus.
When that break is missing, which is 95% of the time in eBooks, it creates confusion and interrupts the reading experience.
I don't need the fancy curlicues that are often used in pBooks, but a gap between the paragraphs or just a short line doesn't seem like it is asking too much of any of the existing eBook formats right now!
Rant over. Well, until someone brings up eBook formatting again.