Resident Evil 4 > Zelda 1
Bioshock > S3&K
Oblivion already beat Paper Mario TTYD. I'm pretty sure Skyrim would rock that match even harder.
Super Metroid/MGS2 is the only matchup you listed I'm hesitant on. Aside from the few heavy hitters, I'll always side with the newer games.
And I was thinking a 32-entrant contest. 2011 was an awesome year for games, so the fewer snubs, the better.
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SuperNiceDog took my lunch money.