I disagree a bit with the action clunkiness he talks about, as I quite like the control system in this game. However, everything else I wholeheartedly agree with, how often did any of you use the drum can or box? Totally unnecessary what with octocamo and whatnot (which as he said, could be totally unnecessary with the tranq gun and whatnot). And while I am a huge Metal Gear fanboy, on my first play through the game I kept thinking, "Damn, there's not much game here...take 10 steps, cutscene, 10 more, another cutscene, the cutscene to gameplay ratio is ridiculous!" And on subsequent playthroughs, I picked out the things that I think should have been left out entirely. The story didn't even fascinate me that much, I just thought "Finally we get an explanation for all the bullshit in MGS2." All that being said, I still love the game, and I love MGO, but all in all I think I preferred MGS3.
And normally I think Yahtzee is just a prick who feels the need to hate on games simply because it's the in thing to do, and you Yahtzee fanboys like it because you think it's new and different and hip, when in fact it's tired and old, but this time I think he hit the nail on the head pretty well.