I don't think the OP actually read the title of the article, or didn't understand it, but it says "30 Characters That Defined a Decade". Maybe you read it as "30 BEST CHARACTERS, EVER, OF ALL TIME".
Master Chief and GLaDOS define the gdecade as what it was. Master Chief was the nearly silent protagonist that helped bridge the gap for counter-strike, half-life playing PC FPS players to consoles. Games like Call of Duty and Battlefield Bad Company 2 wouldn't be the console juggernauts that they are weren't it for Master Chief.
GLaDOS defined the slapstick, random humor of the decade. Without GlaDOS the game would have been memorable, despite the puzzles. However, the puzzles opened doors for puzzle games that take relatively simple concepts and expand them to mind-bending levels. Games like Braid and Super Meat Boy wouldn't near the amount of popularity if the puzzle genre didn't get the spotlight from GLaDOS and Portal.
What did The Boss do? The Boss offered a tragic story in a series of games that were already known for equally tragic things before the decade. The only thing The Boss did was raise the bar for other Metal Gear games.