While I do like both of them, I must agree that I'm really partial to the Japanese Boxart. I love the way Link is actually holding his sword up against the backdrop of the open blue sky. The image seems to have more perspective to it reaching up into the sky than the gold one does, which feels comparatively flatter, and it is more illustriously accurate of the game's title, Skyward Sword, with Link's sword glistening and really extending up straight into the sky. The blue just feels perfect for the game's cover to me, although at the same time, I suppose that might just be a case of personal preference in the end.
I think what I might do is wait for high-quality scans of the japanese boxart to appear online, and then print one out as a second cover that I can swap with the gold one when I want. That should be a good way to balance the two anyway.