Didn't they said that both versions were going to have the same characters? I'd say that by the time they release the WIiU game, there will be more playable characters and are going to release free DLC for the 3DS one.
Oh, and I've always played with Sheik, I guess that's where I'll start.
I think they said it, but it might have just been implied it. We'll see, wouldn't be suprised either way.