So, my two cents.
Certainly the MGS series is convoluted and makes little sense, even after heavy analysis. That's not how Twilight works. Twilight is exceptionally simple...so simple you can say that there is no story. It's just a girl getting hot and bothered about a sparkly vampire.
Most of the hate I see levied against Twilight is the sparkly vampires, followed by teen angst. Certainly the American gamer/horror literature fans hate them for being so sparkly, but remember that modern Japanese vampires (think Castlevania, Hellsing, Blood: The Last Vampire and Blood+, etc...) aren't very traditional, either. Just check out http://www.tvtropes.org/pmwiki/pmwiki.php/Main/OurVampiresAreDifferent for several good examples.
Anyway! I haven't read Twilight, or watched the movie, so I can't really make a comment about Kojima liking it. Though I'd like to say that I was surprised. If, however, what whoever said earlier about Twilight's translated title being "My Boyfriend is a Vampire" is true? No way did anybody pick up a book called "My Boyfriend is a Vampire" and take it seriously.