Also, I'm pretty sure the 3DS has more memory (RAM) than the Wii.
Isn't a chunk of that ram used for running the home menu in the background at all times? Maybe the issue with 3DS isn't that it *CANT* do the transformation characters, but that since the WII U has more ram, it doesn't have to load them mid-fight, so the 3DS is SLOWER by comparison, and therefore the balance is off/different. Maybe he wanted to make transformation actually usable this time (being able to combo a sheik smash attack / zelda din's fire would be nice), but because of the 3DS having to still load from the cart, he can't do it.