True, it was far superior to the Colts, but on paper it never appeared like it "should" be. The Colts had really good individual players - Dwight Freeney, Robert Mathis, Bob Sanders. It isn't a coincidence the Colts won the Super Bowl that year with their best defense of Peyton's run there. The Colts were always weak at LB and in the secondary, and they won the SB that year Bob Sanders was one of the better safeties in the league. Again, not a coincidence. The Colts, even their defense was lacking, always had a D-line that could rush the passer.
Brady is better than Peyton because of Belichick, pure and simple. Brady always has had superior coaching. Belichick never has had an elite pass rusher in his prime - he has had good guys in the secondary like Ty Law or Rodney Harrison, but he's never had an edge rusher that struck the fear of God in you. Would Chandler Jones be the closest thing? As an example, look at the D-line that started Super Bowl LI...Alan Branch, Malcom Brown, and Trey Flowers. I mean are they solid names, yes, but gamebreakers? Does that sound like a Super Bowl-winning D-line?