I'm not really digging the covers to be honest. I think the baby blue and white colour scheme is a little too temperate and inconspicious. I also believe there is still going to be confusion among casual gamers as to whether or not Wii U games will play on their Wii, especially in today's market where a purple 360 box indicates that it's a Kinect supported game. If mainstream media outlets are getting confused, I guarantee you that some people will think they simply need to buy a Wii U controller to play these games. That's more a problem with the Wii U name rather than cover design though.
Ultimately I don't think the box design matters all that much. The design of the covers is the least of Wii U's problems as far as I'm concerned.