You can find faults in almost anything and I'm never going to claim that MGS4 is perfect, but I will tell you that no other game made me FEEL as good while playing it. It's probably the best video game experience I've ever had. No amount of analysis could possibly tarnish that for me.
So, MGS4 is still as good as I think.
But, what you have here is impressive. It's well researched, intricate, and well written. I'd like to see you do something like this for other big games that everyone loves: BIoShock, Halo, Call of Duty, etc. It could be cool.
A score is not a review. I think a less specific review scoring system encourages a reader to actually check out the text of a review. The text will give you the specifics, rather than the score. A score should just tell you whether the game is good or not, it is up to the review to tell you why.