When comparing the two, I believe that you should compare career statistics and head to head statistics (because both players were going against each other in the same conditions with the same type of field).
Here is a look at both QBs' career stats:
Brady: 26,364 yards; 197 touchdowns; 86 interceptions
Manning: 29,442 yards; 216 touchdowns; 120 interceptions
Manning wins the yardage mark by a wide margin. But consider that, even though the Colts had a good running back in Edgerrin James for some years, Manning was throwing the ball A LOT more than Brady. He had Marvin Harrison in his prime and a young and emerging Reggie Wayne to throw to. However, with that said, Manning only threw for 19 more touchdowns than Brady. Keep in mind that prior to 2007, Brady's most dangerous target thus far in his career was Deion Branch. In 2007, when Brady finally got weapons like Manning had throughout his entire career, he torched the league and set records in touchdowns thrown, fifty, while only throwing EIGHT interceptions.
In the interception catagory, anyone can see that Manning loses the argument of who makes better decisions. In that catagory, Manning has thrown a whopping 34 more interceptions. This includes the playoffs as well. Anyone who has watched a playoff game where Manning goes up against Super Bowl calibur defenses knows that he often gets happy feet when the inside rush begins to get to him. When that happens, he begins dancing in the backfield and many times, cannot get the correct footing in order to release the ball with the velocity and accuracy he needs to hit his target. This explains why Manning has had a significantly larger amount of INTS.
Also, while comparing career stats, you should consider that Manning played the 2008 season while Brady did not. Had Brady played, it is very likely that he would have thrown AT LEAST 30-35 more touchdowns. Especially when you consider that the running back situation was the way it was (massive amount of injuries).
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Now let's take a look at the career head to head stats, including postseason, of both quarterbacks since this will give us a look at how each performed while operating under the same conditions...
Brady: 205/314, 65.3-percent completion, 2,275 yards, 17 touchdowns, 11 interceptions
Manning: 228/381, 59.8-percent completion, 2,761 yards, 16 touchdowns, 23 interceptions
Manning again wins the yardage and attempt argument but, despite the difference in the amount of attempts (not as big as I originally thought before checking the stats, to be honest) Manning has thrown one less touchdown that Brady and has thrown for twelve more interceptions. Brady also beats Manning in the completion percentage catagory as well. So, even in the same situations, Brady is more accurate with his throwns than Manning is.
See? I've come all this way without mentioning the Super Bowl wins. First let me say that I will not point to the amount of wins to support my argument because it is not allowed and will take the thread in a different direction than anybody wants to go in, especially when our resident Colts fans sniff this thread out. But I will say that Brady has proven himself much more than Manning under pressure. In two Super Bowl wins, Adam Vinatieri's foot won the game for us. However, as far as I know, Vinatieri isn't capable of hitting a 100-yard field goal. Against the Rams and the Panthers, Brady had to put Vinatieri in position to make the field goal and he did so with patience, calm, and accuracy. He took what he could find down the field and used his time wisely. Ultimately, he and Vinatieri won us those games. In 2004, he didn't have to do that but still had a very solid game for us. In 2007, Stephen Neal went down and the inside rush of the Giants took advantage. Brady couldn't step into his throws and had to make split second decisions before being hit. However, when he needed to take his team down the field and score a touchdown he executed. If the defense had been able to stop a miracle pass and hold the Giants offense, that 2007 team would have won the Super Bowl, gone undefeated in the process, and claimed the label of the greatest of all time.
I will close out this post by saying that, while I think Brady is the better quarterback (maybe I'm biased
), I do have a tremendous amount of respect for Manning. He is an all time great quarterback and has made his team better every year he has been at the helm. Many times he's had to carry his team to the playoffs, as has been mentioned here already. However, all things considered, there is an abundant amount of evidence for why Brady has been the better quarterback throughout his career. I just hope he solidifies it in 2009.