I have been using Stanza on my iPhone for a while now and I think the opposite.

I like the interface and usability of Stanza better. It does have PDF support, annotations and bookmarks. You can load your own ePubs and PDFs into it through iTunes. It has nice dictionary features, brightness controls, themes, support for third-party libraries.

Overall seemed like a much more mature app than iBooks for the short time I spent with iBooks so far.