I agree with your points but I don't think that's what the article is about. The article is questioning character 'creation' making players feel God like. It also asks if the unique characters take away from a good story because you can't write a "one size fits all." I think these ideas are simply wrong. I don't think I'm giving birth or creating a new life form. I'm playing myself in the game much as an actor is playing a role in a movie.
As far as storyline goes, look at Guild Wars and Aion. They render their cut scenes with your character so you are a part of the developing story rather than just watching a character from the story. And both World of Warcraft and Aion have moments where you play in an instance (solo or just your party) where you participate with a few NPCs as key elements of the story unfolds. Your character speaks to the prince, your character is cheered for saving the town and it's your character that fights side by side with Thral. The story is just as deep and you get to play a part in it through your character.
Rather than think storyline is dead because of unique character creation, the author should consider how these interactive stories improve on standard story telling. I've played enough "you are Dr. Freedman" games. I like what is being done.