Personally, I think they were just experimenting. Game design was still somewhat in it's infancy back then. Developers had yet to really utilize controls in creative ways. That, and the amount of buttons were severely limited.
Oddly enough, when people think of each generation of consoles, they always think of the graphical boost. But one of the most important additions to each new console generation was the addition of extra buttons on the controller, allowing developers more freedom in designing control schemes.
Still, I believe a designer of today could, if given the limitations of the NES controller, design a more intricate and ergonomic control scheme than what was seen in the vast majority of NES titles.
Some games stand the test of time. CVII is not one of them. Even so, I still play through it once every 5 years or so.