Realistically the Wii U and 3DS should have ONE VC and certain games are just not available for the 3DS because of hardware restrictions (I'm assuming that Cube games on the 3DS would be pretty hard). If you had to pick one of the two systems for GBA games the 3DS would make more sense but there is no good reason why they shouldn't be on both.
In regards to Zelda, if I was in charge of Nintendo I would push back on Wind Waker HD as well, but only because I wouldn't want to waste resources on a remake when it could be put towards a new game. The VC is for re-releases of the past, the new systems are for the future. I'm shocked that Skyward Sword was even in the discussion as it is not even two years old. It's also worth noting that both it and Twilight Princess are playable on the Wii U so a Wii U version would be especially pointless. If you're going to make redundent remakes that prey on fanboys that just can't resist buying Malibu Stacy with a new hat, Wind Waker is the best choice. While I prefer Majora's Mask, it would be more efficient for Nintendo to remake that for the 3DS since it used the same engine as Ocarina of Time and thus could re-use resources from the 3DS version of that game.