I noticed this very thing when reading through all the editors' GOTY picks. Zelda made very few lists other than the Nintendo editors, and it wasn't even mentioned in any of their "honorable mentions" section. It made me curious, and I went to the Okami review (scored at a 9.1), since that game seemed to be picked more often. I'm going to quote from the Okami review, by Chris Roper...
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It might not quite be on the level of Zelda, but it's probably the closest thing we've ever seen outside of Nintendo.
Now, this game received a 9.1 score. Going by the numbers, LoZ:TP received a 9.5. Different reviewers, yeah yeah, whatever. What's clear is that the other editors, in order to become knowledgable about what else is out there and make informed decisions, need to drop the Nintendo hate and actually play the games before they judge and disregard them.
It takes guts to do what Matt did and call them out, and I applaud that.