Actaully, having used iBooks on my wife's iPhone 4, I can see how some are upset. It seems like Apple just ported the iPad version to the iPhone, which isn't a very good idea. First and foremost, the borders are much too wide. On Stanza, the words go right to the edge of the screen. On iBooks, there is like a 5 mm border along all edges of the text. This greatly reduces the amount of words per per. On the iPad, which has a large screen, but on the iPhone, it's extremely wasteful of screen real estate.
2nd, I really need to be able to toggle to night mode. If they could add this option right under the "sepia" on/off toggle, this would be great. Sure, you can do this by setting up inverse black/white by tripple clicking, but it would be much more stream-lined if you could do it within the app. In night mode, they should also make the top status bar either disappear or turn black. Currently, it stays white and is very distracting. And, again, it wastes screen space. In night mode, they also need to get rid of the white outline of the pages on the right and in the corners. Sure, I'm all for being realistic, but this is still a phone, not a real book.
For now, due to ease of use and stylistic reasons, I'll be sticking with Stanza. We all know how long it takes for Apple to (a) admit a problem/bug and to (b) act on it. So, I doubt I'll be changing back to iBooks in the next 6 or so months.