You're getting to hung up on the nunchuck part. It's not that he would've pulled the plug, but that's not the product they were aiming to make. He just wouldn't accept it, because it would've gone in the opposite direction of his pitch. While announcing Ninja Gaiden 3, TN said that these past few years were rough, but working with Nintendo helped them improve their confidence, not to mention the Iwata asks on how all the team understood each other and comunicated a lot. It could all be a load of bs, but I doubt it.
As for the whole port argument, it's entirely different to downport something that's been made to a system, rather than working from the ground up. All the beautiful camara work, wouldn't have existed, because it hasn't been revised for 15 years. I'd even say that on the GC it would've been the same case thanks to the C-Stick. Sense move, Overblasts and Lethal Strikes are all products of the limitations imposed by the Wii Remote, it wouldn't have worked that way, even 1st person would've been gone I guess in favour of a traditional missile switch system.
This game, is a product of it's time. It couldn't have been created at any other time, even though the theoretical tools are there to make the exact same game on the GC.