I actually consult for Penguin (but also other publishers so hopefully I am not as biased), I am also on the ePub committee and I must tell that at least in it's current form epub is not the solution to all forms of content.
Also Apple tends to do unspecified things to epub deliveries and standard compliant epubs fail Apple check, but it's hard to blame them yet, they're just trying
Moreover it is the publisher who chooses to wrap their epubs in DRM or not so Penguin, not Apple is causing the incompatibilities to some extent.
Amazon is obviously the biggest offender with their proprietary outdated format which is almost the same but not quite an epub.
I also agree that epub is the most sensible solution right now, but like I said it's not there yet and simply doesn't work for non-reflowable content (think anything rich media, graphic or design heavy) which is a lot of content...