Carmack is a great programmer to be sure. Commander Keen, however, was not a better version of Mario. It was worse than Mario in every way -- art, music, and gameplay are all inferior.
Nobody outside of Gen X PC gamers know what Commander Keen is. Everyone knows what Mario is. While copying may be the way design works, copying only gets you so far.
The article didn't say it was better. No one thought it was better. It was just the first time anyone was able to smoothly side scroll on a PC. By copying something, he was able to push the boundaries of the perceived constraints of the technology which I believe is what the article is pointing out.
To add to this Commander Keen was released on a very limited platform. More people were gaming on Nintendo systems than personal computers. If Commander Keen was released on Nintendo things may have gone differently.
Even if that were true (and I don't think it is), Commander Keen should be compared to Mario 3 (which still came out over a year earlier than the first Keen), not Mario. And 4-6 are most appropriately compared to Super Mario World, which was released the same year.
Keen was/is great, but Mario 3 and Mario World are on the shortlist for best game ever.
Nobody outside of Gen X PC gamers know what Commander Keen is. Everyone knows what Mario is. While copying may be the way design works, copying only gets you so far.