The fact people still talk and debate about the game's story, characters and it's themes more than ten years after the fact says a lot about it. There's much more to the game than simply "whatta twist!"
I would not say SH2 has the greatest story in video game history. It certainly has an ambitious one. I think it's quite compelling and I don't fully understand the story. I've read explanations, or possible explanations on the web, but I don't think I want it explained to me. I will hopefully play SH2 again. Maybe around Halloween!
SE may have another FF hit on their hands with FFX/X-2 HD. Perhaps the biggest FF since, well, FFX. :p