To me, the elimination of race as a factor in character build is the biggest functional change to the game since AD&D ended the D&D "race as class" mechanic and was really the biggest mechanical difference between the various numbered editions of D&D and the B/X & BECMI games which were really the truest decedents of OD&D and Chainmail. I suppose the 3x3 alignment matrix was also different, but it was as irrelevant to the mechanics of the game as it still is today.
It may not really matter that much, but it is a pretty big shift in the flavor of the game.