I think the 3DS menu is just fine:
-It's compact which is perfect for a touch screen
-All the colors play nicely together (red compliments green, orange compliments blue, the pinks and purples are light enough to not clash etc)
Now, the Wii U menu should be a little different. Something more akin to Melee with it's digital feel, however I don't want to go back to purples and yellows because that's a bit too easy. Imo, something involving more neon colors would be pretty nifty especially with the static-effect that the Melee backgrounds had.