If by "upsets" you mean "lower seed wins" (which seems to be your definition):
Ike/BK over Conker/Poo
Bartz/Gilgamesh over Guybrush/LeChuck
Leon/Ada over Subby/Scorpion
Big Boss/Boss over Tidus/Jecht
Pac-Man/Blinky over Crash/Cortex
lol Hitler's in a GameFAQs Contest over Sora/Riku
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