Since many (most?) of the issues with the clouds are getting written off for various reasons, not all of which I disagree with, I'd like to focus for a moment on the crystals, because this is one of the discrepancies that stands out the most to me.
These crystals are very bright blue, and contrast very well against the dark background, making it difficult to argue the detail has simply been lost from overexposure. But look specifically at the rightmost crystal formation, and you'll notice the crystals have a clear break in the leaked image and are missing the leftward slant of the crystal formation in the official banner.
This crystal formation is almost entirely covered up by Ivysaur and Squirtle in both the original E3 banner and its current version.