My problem is that I've been spoiled by Stanza and eReader.
The iBooks, Kindle, and Nook apps are all very weak as readers and when it comes to customizing the reading experience. They drive me up the wall with their required full justified, limited night/color schemes, no cut and paste of quotes to a separate notebook app, animation on page turning, having to swipe to turn, etc. Every couple of months I try them and discover that they still haven't fixed these basics (the deficiencies vary by app) and give up!
If I could buy Amazon, B & N, or Apple books and readily read them in Stanza, I'd be fine. Or, if Barnes & Noble hadn't dropped book buying and downloading from the B&N eReader, I would have been all set. As it is, I still am not buying ebooks because I'll end up trapped in one of the stores and one of those deficient apps-- and won't have a good reading experience!
deliverator made a superb point; one that I had forgotten about in my testing.
"I move back and forth between my iPad and my iPhone, and I have had too many experiences with Kindle where I accidentally went forward in a book, or maybe checked a footnote, and from that point on Kindle only will only sync to the end of the book, because that was my furthest position. Infuriating."
Absolutely an issue.