Honestly its getting rather annoying to read the comments to every list. The thoughts posted are rarely illuminating. The same nonsense every time the people that only own a Wii think that Mario is the second coming of Christ, and to not have him on the alter at one is some sort of crime against humanity.
Super Mario Galaxy may be the greatest platformer to come around in years, but its still a platformer. That means it suffers from the same weaknesses all platformers suffer from. Chief among those is replay. Most players will play through a platformer once, and the more intense might play their way through a second time. However the magic is short lived, and can never be recaptured.
Basically all you need to kick Mario out of the top spots is a reviewer that places a higher value on replay. Such a reviewer will give greater kudos to a Halo 3, Orange Box, or a Mass Effect. All games that could end up tipping a players time commitment into realms of hundreds of hours over the lifetime. Where a Mario will struggle to capture thirty hours.
Kind of tired of every list being about Mario. He makes the list high good for him if no well the reviewer isn't a fan what you going to do. There are legitimate reasons for Mario and against Mario. Hardly a case of Mario doing everything perfectly on all fronts. Just as the Halo 3 single player mode was hardly epic, or the tragedy of Bioshock not having a multiplayer mode even though the game begs for one.