They beat Sabbath in last year's tournament, so it doesn't surprise me, although I of course don't agree with the result. The Neurosis loss also surpises me, but the Novembers Doom one is a very good album (I still say they've improved with each one, though I haven't heard Novella yet), and they have that Heathen Crusade boost...not that it helped Vried any.
Immortal got my vote simply because I listen to it more than GC. And that's about all the logic I used in this case. Same applies to Symphony X. The truth is, Disillusion possibly is the better album where V is just waaay too long, but damn, that was the toughest vote.
While I truly enjoy that Disillusion disc, I don't think it holds a candle to V. From the songwriting, to the musicianship, to the lyrics, and of course Russell's amazing voice, V is superior (for me) in every way. That said, the one criticism of V I will accept, is the one you made. While I don't think there are any weak moments on this disc, had they cut the 5 - 7 of the least wonderful moments, the disc as a whole would be stronger.