Yeah, the new one has the Wii Remote jackets inside as well as a slightly updated copy of Wii Sports. The loading screen now shows the Wii Remote wearing its jacket and I swear it feels slightly different. The mechanics of Boxing felt slightly more fluid? That's probably just wishful thinking though.
Oh, the clear circular plastic base is also "installed" into the grey base in the new boxes.
We picked one up for my cousin and I was confused as we set it up, thinking, "Mine didn't come with one of these . . ." Of course, I had just ignored the stand on the bottom of the box when I tore mine open.