Brees is awesome, so this is not an argument against him so much as it is one for Elway. Sure, Elway never threw more than 27 TDs in a season, but Joe Montana only did it twice (and 31 was his high). Quarterbacks back then didn't throw for as many TD's and yards as they do now, Marino in '84 notwithstanding.
But they still had to throw accurately. Throwing the ball hasn't changed. I watched Elway's games also. He never really lived up to the hype. The teams that won carried him long after his prime. The reality is that the running game and defense carried those teams. Although Rod Smith, Shannon Sharpe and Ed McCaffrey were not anything to sneeze at.
How can you say that Brees won with sub-par receiving talent, while ignoring that Elway did that for most of his career (until he Pro Bowl and HOF talent at the skill positions in the 90's)? Heck, Michael Thomas is better than any WR Elway ever had.
Elway had the 3 Amigos, Rod Smith, Ed McCaffrey, Vance Johnson, Shannon Sharpe. I could argue Shannon Sharpe would be as good as Michael Thomas if he was in the same passing system MT is in (and that Marquis Colston and Cook thrived in)
Plus, Elway played his career outside in the cold in Denver, while Brees has played inside in a dome for most of his career, and I believe the numbers have shown that Brees isn't the stud QB outside that he is inside.
Thinner air? When the Broncos win they are gassing opponents. Many people say that is an advantage, It cuts both ways. Brees has been remarkably consistent and accurate and quick to get rid of the ball. I could see an argument for Peyton Manning, or Brady, or Favre, or Joe Montana, or Dan Marino, or even Steve Young before I can see an argument for Elway just based on his football career.