Ico over Shadow of the Colossus...
Metal Gear Solid 2 over Metal Gear Solid 4...
Legend of Zelda over Ocarina of Time...
World of Warcraft over lots of better games...
Wait, Okami is that low on the list?
Why is Final Fantasy XII there?
Since when is the original Castlevania better than Aria of Sorrow?
In what universe is Beyond Good and Evil only #200???
People, Final Fantasy II and III are actually IV and VI, okay? Get that into your heads!
Okay... yeah, this list is screwed up. It has all the games it should have, but some that it shouldn't, and definitely not in the right order. I know this is largely a matter of opinion, but come on guys.
And really, "influential" and "best" are not the same thing. Games like the original Legend of Zelda and Metroid simply do not belong on that list: sure they were influential, but countless better games have been made since then.