Most of the QBs that have won super bowls fit the Tom Brady mold much more than they do the dual-threat QB mode. Their athleticism is usually not as great as the dual threat QBs. So, they have to learn to play smarter than the other QBs from a young age. They have to learn to stand in the pocket and find receivers and throw it with bodies all around them.
When the game gets dumbed down for a lot of the dual threat QBs, they aren't able to beat good teams when it really counts in the playoffs.