The font-variant is a fault of ADE, not of the Nook. I agree that it should be there.
The automatic indent is probably part of the default stylesheet, but it should honor if you specifically set the indent to 0.
I am not familiar with the photo's, so no comments there.
CSS3 is not in the IDPF specifications, so the Nook is totally correct in not supporting it. In fact, the iPad should not honor it, since it is not part of the specs. In fact, I think that >90% of the readers will not support it.
I suppose it is 'nice' that iPad ignores the standard... However, iBooks does not support ePub, but rather iPub...