Ali had a much faster rythm than Holmes. That, for me, is the greatest difference. In his prime, he was able to move relaxed in that fast rythm and react to every movement of his opponent. Holmes did way more leading, and was more speculative instead of reactive.
Holmes had a better jab, better right hand and didn't rely on his speed as much, as shown later on his career. He may of been the more complete fighter.
Everything. Mr. Ali was so fast and brilliant, the left hooks he got hit with were actually strategic face butts to his opppnents' hands. Slow motion video confirms this tactic, proving he was in fact unhittable. His will to win was also superior. He would win by damaging any part of the opponent necessary- hands, psyche, face, feelings, you name it. Mr. Holmes was only good for a dropkick in a track suit,which Mr. Ali surely would have delivered better, even if it missed.