True, I never played Sin & Punishment on the N64. I don't blame the developer for the Wii controll schemes but the the fact of the matter is the game still has a learning curve and the controls are cumbersome. However, they are easy to get used to with some practice.
For me, I found Sin & Punishment's controls to be fairly complex at first which prevented me from thoroughly enjoying the game using the GameCube controller with the game's 3rd control scheme setting. I eventually mastered it so the controls feel natural to me.
As for the N64 controller, Treasure stated that "The idea behind that project [Sin & Punishment] was basically to make a game that used the left-hand position on the Nintendo 64 controller, since not too many other games did that."
Here's the article.
http://www.1up.com/do/newsStory?cId=3176363