The biggest victim of the old system had to have been Penn State or Auburn. Undefeated and unrewarded seasons in '68, '69, '73, and '94 for the Lions, and the same for AU in 2004, plus probationary 1993 as well as being leapfrogged in 1983, despite being the highest-ranked team to win their bowl and having face the nation's toughest schedule.
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Penn State may have been viewed as a 'less than' in the late 60s (or not, idk), but they had the Heisman winner in '73, just the bad luck of nearly every helmet program having an undefeated regular season (with undefeated OSU and UM tying). But 1994 made no sense. To this day, I consider them a split NC with Nebraska.
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Auburn in 04 just had the bad luck of being 1 of 3 undefeated teams, plus USC blowing out OU, plus having a ho-hum win over VT itself. The 1993 team was never seriously considered for the NC, because it wasn't FSU or ND. 1983 was a farce. Miami lost it's first game and Auburn lost its second, so both were on long win streaks. Yes, Miami slayed Goliath Nebraska, but Auburn closed its season with wins over #4, #5, #7, #18, and #9. Consecutively.
There's no rational argument for Auburn not being the 1983 NC, at least not behind Miami.