The whole thing with INDY in the Dungy era and then Polians mess, was we will out play you, not outscheme you. It allowed them to get just guys in the draft, without any real talent, and plug and play with simple scheme's and just say here we come, try and beat us.
The problem is, without Manning's control over the offense, to get in and out of the right play, the offense could not cover its role last year. And, the defense had NO secondary to cover let alone play the run good enough, even with its "starters" the last 2 years.
They fell apart at the seams with a combination of putting all their eggs in one injury away screwed basket and poor attention to personnel on defense the last 4 years. They never replaced Sanders or their CB's appropriately and it made their pass rush less effective as teams could 3 and 5 step them to death.
DEN does not have that problem right now. They are actually much better suited to how Manning wants to play, and better on the back end suprisingly.