Every metric in sports in flawed and none are perfect. But you need them to come up with numbers for any player. Do other factors come into signing a QB moreso than other positions? Yes they do (see Ryan Fitzpatrick and Matt Cassels contracts), but you have to have a baseline for comparing players. The teams regularly battle over numbers, the supporting casts they have, and what those players mean in the grand scheme of things.
OK. Brady generally loses the supporting cast battle from an overall talent supporting cast standpoint. That translates into a win comparatively speaking for the purposes of assessing his value.
Brees essentially means the same thing to New Orleans as Brady to New England. They are the whole offense. They run similar offenses when you breakdown their pass selections. They have identical regular season records. The Saints run more offensive plays and Brees puts up nutty yardage.
Both take what the defense gives them yardage wise. What that yardage translates to, however, is what really matters.
Nobody goes back and looks at stats from 2006 and 2007. If they did Favre would still be in the NFL. Its not a question of who is better for his career. Brees isnt even in the same ballpark as Brady and Manning. He has a terrible playoff record and has his share of losing teams he played on which was never the case for the other two once they got experience under their belt.
OK. I'm good to go on last 3 even including Brady's rebound season from the ACL. Brady's consistency is part of his value. He plays well in all settings. He plays well hurt. Brees may not be hurt as often, but when he is the wheels fall off the wagon to a greater extent. Durability matters, but in a league where almost everyone is hurting on some level over the course of a season, how well you play through that is part of the durability assessment.
Teams, for the most part, look at the prior three years. Where QBs get more of a pass is that they discount injuries much more when signing contracts (Manning, Pennington), whereas its devastating for other positions on the field where they are treated as finished. They also go back and compare statistics when contracts were signed. The real comparison for Brees is Brady post-injury in 2009 and Manning pre-injury in 2010. How much better was Brees when those guys got 18 million dollar deals?
You're mistake here is in comparing Brady in 2009 when his deal was signed in 2011 - making 2010 his year to which Brees 2011 season should be compared. Brady didn't throw for a ton of yards in 2010, but he somehow managed to be league MVP too. And looking at a pure stats adjusted for level of opponent metric, as FO does with their stats, Brady ranked #1 in both DYAR and DVOA that year. Brees at the same time ranked 5th and 12th. That was his 22 pick season, something Brady has never approached no matter what injuries or circumstances he was being asked to play through.
In fact over the all important last 3 years Brady has ranked more consistently (always within the top 3 in DYAR and DVOA) if not always higher than Brees. And in an offense otherwise in the midst of personnel flux and transition being asked to front a defense being overhauled in full blown transition... Brees has ranked as low as 12th in DVOA in 2010 and outside the top 3 in DYAR in 2009 and 2010.
Meanwhile, impressive as Rogers has emerged to be, he's got to do it for more than two regular seasons and one post season before I rank him ahead of Brady for any meaningful purposes. He was in the top 5 in DYAR and DVOA in 2010, in the 20 in 2009. He's younger but he has yet to prove he can be consistent over the long run. He was abyssmal this post season, not that Brady or Brees are ever perfect. But they've both shown the ability to rebound, either from individual or team performance failures. Rogers is poised to now but he isn't there yet.
If you wanted to compare Brady in 2007 to Brees today, Brady would still be the highest paid player. New Orleans would not have gone over the 18 million number because there was no way to justify paying Brees the same as Brady, even taking the importance of the player to the team into account. If Rodgers already had a contract extension Brees would have fit somewhere between Brady and Rodgers rather than re-setting the market. I cant recall one agent or anonymously quoted scout/GM in the last few months that said Brees would make less than either Manning or Brady. It was always a given he would get a bigger contract because of those numbers he puts up.
I don't put a lot of stock in agent or media speculation or annonymous scout banter because it's largely subjective and/or perception based. And last man up usually tops the position irrespective of actual comparative value. Eli reset the bar in 2009...and he still struggles to crack most pundits top 5's, while back then aside from the ring he struggled to make top 10's. Just like the most recent shiny new QB's drafted used to impact the bar before the new CBA was entered into. Before Brady and Manning did their last deals (in 2011) the media and agents were convinced one or both would top $20M, perhaps by as much as $4-5M. Didn't happen. And anyone who understood the model and where the CBA was headed knew it wouldn't because the model wouldn't sustain it.
As for PFF, Im not sure why you guys discount it so much. I used their basic pass scoring system for the sake of simplicity but the work they do is actually very good. I adjust alot of their stats for other things, such as pass protection, pass rushing, coverage, etc... but its a good database for numbers, I just think some of their statistical takeaways need adjustments. Their basic grading system is very similar to the way most NFL teams review game film. That doesnt mean its free of flaws (a good/bad play is always going to be subjective especially without knowing the playcall, and rating players per play rather than an aggregate total would normalize the numbers better) but its a tool that can be used to take a bigger overall look at a player.
