Cloud-synced bookmarks and notes - preferably with a social profile like that of Kindle[1][2]. The way I read books is to make a lot of notes and highlights; I know some people don't do this, but this helps me summarize books more easily and "reread" them, if I need to. Picking out your favourite passages of
Aesop,
The Art of War and
The Prince is extremely convenient. That not how everyone reads and digests books, but it's definitely how I do - and I assume that many students will want to do the same with their textbooks.
The book selection is also very meagre[3] (at least in this country), but more important, some of the available free books are typeset from hell. It's just a copy-paste of Project Gutenberg and similar endeavours, which are not formatted for iBooks at all. This does not inspire me to buy any iBooks, and it leaves me to wonder how the (free) book user experience can be so bad, when Apple make such an effort of vetting apps from trivial ailments.
Another, perhaps minor, thing is that I can't highlight across pages, which drives me absolutely bonkers.
If I were an author (or worked for one) and wanted to release a book on iOS, would I distribute it via iBooks or create a native app for it like Al Gore did? I honestly don't know, and I have a feeling that my hesitation has more to do with the shortcomings of iBooks than the allure of making a standalone app.
[1]: https://kindle.amazon.com/profile/Craig-Mod/52461
[2]: I'm sure it would be in Steve Jobs's best interest to make us forget Ping as soon as possible. Better to replace something vapid with something slightly high-brow.
[3]: It doesn't even have A Song of Ice and Fire!