I'm not sure what you're driving at. Are you saying that Bioshock and Bioshock Infinite are like System Shock 2? Or are you saying that they're prime targets and reference examples for examining what's going wrong?
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