The way I see it, Kowaliski is making a parallel between an oldschool Ken Levine designed game, and his latest one. That's mostly the reason SS2 and BI are mentioned, really. Well, and the fact that it's a BI rant.
Gotta admint, I feel pretty much the same about Bioshock Infinite's shooting gameplay. For me, it's lacking. But, in combination with the audio-visual and story aspects, it's really on another level than most FPS games today. So it's a better game than any military shooter today, even if you shouldn't compare them on some levels.
As for SS2, man, I'm in love with that game. And I can still say the shooting mechanics are not very good at all. They haven't aged well, and weren't that good even then, from a purely shooter standpoint. System Shock 2 is more of a first person survival RPG mashup thing than a straight up first person shooter. Same with Deus Ex. And STALKER. I just think this needs to be said and taken into account.
The Bioshock games are straight up first person shooters with everything else streamlined and dumbed down. Or maybe in other words, they have crystallized the shooting mechanics and tried to make it all more dynamic. I'm not getting into why they did it.
There are still some very fun first person shooters today, I can't argue with that. But System Shock 2 was an extremely well made mix of different genres, an interesting story and different gameplay mechanics (most of which aren't necessarily related to the FPS genre). This is what's lacking today in games that are mostly first and sometimes third person in perspective and are relying on the shooter aspect for interaction.
Maybe I'm just saying rubbish here, but I believe that the "FPS" abbreviation is a bit outdated, or at least somewhat problematic. Making comparisons between Call of Duty and Dishonored just creates even more useless debate. As is comparing System Shock 2 to Bioshock Infinite.
Personally, I'd like a bit more of SS2's design and ideas implemented today, a more complex mashup of genres, but that's just me. Complex doesn't necessarily mean better, but it can damn well help. It's just that nowadays we have something called a (freakin' huge) video games industry, so the priorities are mostly different.