I applaud your thread. There has been a couple of these threads in the past, but I never felt the need to reply because I didn't feel like thinking up all these box-art. You however, posted most good ones right there in the OP, for me to pick. Thank you .
I like the more artsy ones, that aren't too cluttered for the sake of being cluttered, have a balanced color palette and that have a clear focus with a good logo neatly placed. For example I don't really like the art for Smash Bros and think the 3DS one is better because of it's composition. The Bayonetta 2 (EU one is a bit better though) and especially New Super Mario Bros. one are all over the place.
I think the best ones are the Wonderful 101 art, the Xenoblade X art, the Fatal Frame art and the Pikmin 3 art. Of these, I'd say Fatal Frame is the best one, because of it's interesting composition, the integration of the logo, the strong yet simple nature of it and the mystery.