The people who made Bioshock (which, it should be noted, a lot of them also made System Shock 2) claim BioShock is like System Shock 2[1]. I don't think it's crazy to use it to either refute or reinforce the author's argument -- it's clear the games share some of the same DNA, but there are clearly changes as time and technology marches on. I do think it's kinda weird just to ignore them, though.
Perhaps the author never heard of them (in which case: I want a rock like that!), or more likely, didn't play them and did not want to speak from hearsay, or even more likely, simply didn't afford a thought to them while in the middle of their rant-typing-spree.
I'd grant them that Bioshock shares many of the elements that are praised about System Shock 2. Bioshock Infinite sounds like a great example of sequel gone wrong on the aspects the article's author dislikes.
1) http://pc.gamespy.com/pc/bioshock/707256p1.html