I was trying to figure out which reader was preferable, too. I've been using Stanza on my iPod Touch since before iBooks was an option. I now have iBooks on my iPad, but I think I still prefer Stanza because:
- Stanza has a more customizeable display (especially for white on black reading and margin control)
- I can access my eBook library wirelessly in Stanza
- I can get books from multiple on-line sources into Stanza without syncing through iTunes.
- Stanza seems to handle certain metadata fields better than iBooks (I think my Series info, for instance, transfers from Calibre to Stanza well, but does not transfer to iBooks, or at least iBooks will not use/display that info).
To me the most compelling reason to use iBooks is the page syncing across devices. At the moment I only have one device capable of running iBooks, so that's not very compelling. I also converted a book to epub that had lots of endnotes. iBooks handled the links between endnotes and the main text well, but Stanza did not. There may be a fix for that. I haven't looked into it, but so far that's the only reason I've seen to prefer iBooks. That and it's pretty, but once I'm actually reading, I prefer no distractions to pretty page animations.
Some pros of Stanza over iBooks are discussed on the last pages of the thread you pointed to and on a thread I recently started on the same issue:
https://www.mobileread.com/forums/sho...d.php?t=101852