I took the jailbreak route and will persist with Stanza for a while, at least until the next iBooks update. iBooks needs a few more configuration options and a few more font choices, and it doesn't seem to render italics nicely.
I found the scrolling/paging in Bookshelf very irritating. Kept jerking me out of the reading reverie into wondering WTF I was up to! Readme ignored italics in the book I tried which made it useless. So Stanza remains #1 at the moment for me.