I can't agree with MGS4 being #1 because to me it's not even remotely close to the quality of the original MGS. Snake is barely even a character in MGS4 and everything we have to relate to him by must come exclusively from the previous two games featuring him because he's nothing more than a brooding, quiet old man in the final entry. He doesn't joke, he barely speaks, and he merely gives a listening ear as everyone else explains to him textbook style exactly how they're going to tie up the numerous loose ends. MGS4 feels like that last half hour of extended endings in the Lord of the Rings: The Return of the King that just would never end. All of the best elements come from the parts where people finally shut up and let the emotions ride high. Snake in the microwave was fantastic, the final battle was also. What wasn't was watching Naomi simultaneously die and explain what's going on.
Overall it was a fantastic game, but just cannot handle being anything other than a shadow of the original. Look at the bosses. They are actual rehashes of bosses from MGS, except with no personality this time. Also the most popular act is usually Act 4 and that's no surprise why that is.
ICO and Shadow of the Colossus deserve to be up there.