When looking at an entire issue (after tapping top right to zoom out), sometimes when you scroll left or right, the displayed articles behave erratically and sometimes don't appear as they should. This kind of disrupts the smooth experience expected when using an iPad.
Also, when in normal mode (at page level, viewing and swiping articles) there is a similar problem - sometimes the incoming image doesnt ease in smoothly, but just appears already in place.
I have a 1st gen iPad - not sure if the faster iPad 2 processor reduced this issue.
Finally, inline text and images (within a window) could exhibit a bit more 'bounce' when the user is moving them around (i.e. when the content reaches the end of the frame). It currently just stops rather abruptly. I'd compare it to closing a kitchen drawer with a 'soft close mechanism' (nice and slick and smooth) vs closing a drawer without (abrupt stop, no momentum or intertia).