To expand on the scheme, and how it has improved Denver's running game, consider this.
Denver ran for 244 yards at a 4.4 average. They ran out of the shotgun 19 times, which is obscene in an NFL offense. They used four different positions (HB, QB, FB, FL) and six different players in those 19 runs, keeping the defense off balance. The long TD pass to Decker was out of the shotgun as well, a play that was set up by pounding the ball over and over out of that formation. The Tebow TD run was also out of the shotgun.
This scheme is why Denver is able to run the ball better under Tebow as opposed to Orton. They are essentially letting Tebow run the offense he ran in college.
Now, when you combine a grind it out running game that keeps the clock moving, and eliminate turnovers (Tebow has ONE INT in over 100 pass attempts, which is a league leading INT%, so it's not just "he doesn't throw the ball so doesn't throw INT's"), why is anybody surprised that the defense has played so much better? I'll tell you why.
It's a fucking illusion. It's the same defense. The same players. But when you don't turn it over, play the field position game, burn the clock, and keep the D off the field, well, you get it. Tebow does help the defense, where as Orton was killing the defense.
Will the league catch up? Probably. They always do. But I think Orton vs. Tebow has been put to bed for good. It's not even close, really.