So games 2001-2010 were eligible? Suprised Halo: CE isn't on the list, as you wrote in OP. Also the Super Mario Galaxy omission is weird. Oh well.
Of those listed, I would pick Half-Life 2.
My own games of the decade list would look something like this:
Halo: Combat Evolved
Resident Evil 4
Half-Life 2
Ico
Metroid Prime
Metal Gear Solid 3: Subsistence
BioShock
Super Mario Galaxy
The Legend of Zelda: The Wind Waker
Metroid: Zero Mission
Edit: Oops! It's the best games since 2002. That's a strange starting point. OK, delete Halo: CE and Ico from my list.