Actually, I prefer the USA/PAL cover.
I really like the JAP cover and I would prefer it as background over the other ones, but as for a game, I think the USA/PAL cover works better. It shows exactly what this game is about. Samus, with it's dark alter ego in a grim galaxy.
The japan one just shows all the characters, but I think it fails in showing what the gameplay is all about in one eyesight more than the european/american boxart.
I still love the japanse cover art as picture on it's own though, definitely.