The point was that there is a way to do "objective" study of Human-Computer Interaction, with game controllers as well as everything else, and then there are random opinions offered as "objective" for no reason other than people not caring about what "objective" means.
But you're right about those controllers being somewhat shit. In fairness to the amazing Atari research labs that were used as part of a perhaps poor comparison, they had nothing to do with the design of those controllers and weren't around long enough to really affect much on the hardware side before their iteration of Atari died. For a couple of years Atari had some amazing researchers, but they would have benefitted from some amazing (or merely competent) senior management as well.
2600 and 5200 controllers say otherwise.