Gamesradar state that "it’s just brutally gratifying enough that we’ve decided we don’t really have a problem with it." They aren't being biased, people should read the article before naming names
You play as a totally different person seeing as you die at the end of the good ending. You go back to unravel the truth behind rapture: A gay conspiracy theory related to the nazis. Hitler was Ryan's father teaching him about special camps where they tested on people leading to the descovery of ADAM. You then meet a man called Roonie. He says he is an archeoligist who is trying to uncover the rapture. He asks for your help, you do a few missions for him and accidentally activate rapture to surface. Roonie then reveals that he is Ryans son and that he is trying to rebuild rapture; but unlike Ryan, is trying to take over the world and restore Ryans name. You end up killing him and have the same choice as the first Bioshock.
I agree entirely with this article. If people think mgs has a good story, they have never read a good book or watched a good movie. Games should not have cut scenes, it means that they're more mixed media than a game. I think because games are a lot newer to books and movies, it's going to take a bit longer for story telling to really shine in games as a medium. I'm surprised they didn't mention cod4 because that had no cut scenes and was quite effective in story telling.