The biggest flaw Metacritic has is that they don't add nowhere near the amount of games and reviews that Gamerankings does. So Metacritic often overlooks lesser known games that have been rated high.
One example is "Wings of Power II - WWII Fighters", which came out for PC in 2006, and on gamerankings it had 3 reviews:
88% - PC Gamer
92% - PC Gameworld
98% - Game Vortex
It had an average well above 90%, but since Metacritic only allows games with 4 reviews to have a meta rating, then "Wings of Power II - WWII Fighters" is simply just not ranked.
There's dozens of examples like this one when we're talking about PC games. The Luxor games, Eternal Eden, Samantha Swift all have been released in the last few years and have an average of +90%, but since they don't have enough reviews they're ignored.