Yeah, people will try to brand you here as they tend to do but you're 100% correct. The wiimote is very comfortable when held like a regular remote, but "NES style" is unnatural AND unbalanced due to it being heavier on one side thanks to the batteries and the dip on the other side thanks to the B button. It's a terrible unergonomic design that wouldn't pass muster even if the design team was high. But, if you say this, you become branded a "Wii hater" who is just looking for things to complain about.
Rule #1 of controllers: It must be ergonomic.
If it is not, you have right to complain. I agree with you they should have had a GCN controller option, SPECIFICALLY due to where the game came from, but what can you do? Imo, it's not gonna stop the pure awesome of Super Paper Mario.
Not that I know of? It would be nice, although I would have to then buy a classic controller