I think that basically every team that played them at that time was at a conditioning disadvantage. The defenses that weren't simply roasted by their speed (like Dooley's Tennessee team) were eventually worn out by the pace of play. Correct me if wrong, but I think at some point during Kelly's tenure they tweaked the substitution rule where if the offensive substituted, then the defense had to be given a chance to substitute (official would stand over the ball at the LOS and allow the defense's subs to come onto the field). That of course is the way it should be, but initially that was an even bigger advantage for offenses that ran a HUNH - they would be able to substitute and the defense wouldn't.
Kelly's Oregon teams really only struggled against teams that could match their speed and/or played very physically against their undersized offensive and defensive lines, like LSU, Auburn, and Stanford. LSU, Auburn, and Stanford (especially Auburn and Stanford) also had good offenses that could help control the clock and keep their defenses off the field and rested.
Wait until Pruitt plays in a NCG and has 3 years in a row finishing in the top 4 before you say he's better than Kelly.