While I can see how Hideo Kojima can be looked at in the vein of a film-like auteur I think stretching things way too far. It's hard enough to argue anyone in the film industry anymore is an auteur anymore - let alone in the games industry. He certainly does not fully contribute every single artistic aspect of his games - there's plenty of other people involved such as Yoji Shinkawa and Tomokazu Fukushima. The entire bomb freezing part of the game was conceived by another staff member.
Not that I'm disputing most of what this article has to say - Metal Gear Solid 2: Sons of Liberty certainly was very deceptive and really honed the idea of the digital age home. The concepts of the digital world being able to be manipulated and information censored was a strong concept. It's still very much relevant - with governments looking at (or implementing) internet censorship and preventing the release of certain kinds of media we're already seeing these types of situations. (Well not to the extent of MGS2 of course.)
Can't wait until the Metal Gear Solid HD Collection comes out!