I've been playing with the new iBooks app yesterday and this morning and so far as I can tell it did not add any new support for Epub 3. Even though iBooks Author is supposed to have better support for creating math equations, the iBooks app clearly doesn't have similar support for displaying the equations. MathML clearly is not supported; I tried the requisite Epub3 sample and I still cannot see the equations.
Update: I've gotten a report that MathML is supported. Baldur checked one of the Epub3 demo files on his iPad 3 and the equations did show up. I still cannot see them on my iPad 2.
I'm also not seeing any change in how well iBooks supports things like Javscript, testing widgets, or other interactive features found in the Epub3 spec.
But one thing I have noticed is that the app seems a lot slower on my iPad 2. For the larger ebooks I have seen a noticeable slowdown in responsiveness, an increase time to open an ebook, and even a lag in the time it takes to turn the page.
But at least this app does have access to new dictionaries for German, Spanish, French, Japanese and Simplified Chinese (iOS6 required). And the app can now receive free updates to purchased ebooks - including new chapters, corrections, and other improvements. There are also new sharing options (the usual Facebook, Twitter, email, Messages).
IMO none of the new features outweigh the poorer performance. Nor does the new scrolling mode, though I am amused to see that feature be added.
Scrolling pages is a viewing mode which PDF apps have had for a while now. The reason it's still around after all these years is that it is useful for certain types of reading, and that's why Apple added it to iBooks. But it's not as pretty as the faux page turn which Apple integrated into iBooks, so when Apple added scrolling mode they decided, for the first time in a long while, to let function (features) win out over form (prettiness). I find that amusing.
In all honesty this update is one step forward, 2 steps back. I wish I could downgrade.