One thing I do like about iBooks, as pointless as it may sound, is that it keeps to what I believe is the actuals page structure of the book, whereas the Kindle uses a "location" designation that I believe corresponds to the line number.
Also not keen with the seeming inability to sync my entire kindle library to my iPad in one go...so far it seems I have to do each book individually if I'm on the iPad app.
This location designation is messed up and was one of several reasons why I got rid of my Kindles.