Because Long was a more prolific QB. Their proficiency at playing the position is the key. The Heisman rarely goes to the best player these days (Larry Fitzgerald, Adrian Peterson, Darren McFadden, Colt McCoy, and Ndamakung Suh say hello). Long was competing against Bo Jackson, one of the best to ever play the game. And he almost beat him for the trophy.
I didn't actually get to watch Long play (I'm only 20), but my dad has told me plenty of times that watching him throw the ball was like watching surgery on a football field. That does not fit Stanzi.
Winning a national championship and a Heisman does not make Stanzi a more talented QB than Chuck Long.
Presumably, by "prolific" you are referring to stats. That's a fair point and certainly true. Further, not many Hawk fans need to be convinced that Chuck Long is the greatest Iowa QB ever, particularly those of us that grew up watching him (your dad was right). I do think, though, that if Stanzi were to finish his career with one of those two accomplishments, I'd be inclined to say that his career was more impressive.