My main problem was with him listing Gears of War. Because that's one of the most bland VG stories of all time. Fallout is top notch, Halo is a pretty deep universe so I can understand being drawn into it, and I've always enjoyed Dead Space. But Gears of War is just awful. To continue your movie comparison, it's like saying that Transformers 2 has just as good a story as (for example) Inception. To me, GOW has very few redeeming features - it's just weak character after weak character, cliche after cliche.
But anyway. I'd agree Rapture is more messed up than Columbia. Columbia has the remnants of a functioning society, Rapture didn't. And the 'bosses' in that game were nutjobs. And the whole concept of Big Daddies and Little Sisters was messed up, too. Though Handymen are pretty weird, and Skyhooking people in the face is pretty horrific. Infact, I'd say almost TOO horrific - it's kind of jarring with the subtlety of the rest of the game. Then again, I suppose that's to show Booker off as a bit of a nut, which makes sense.