Tom Brady is in the best situation to be more productive before his playing days end. He has better weapons than Brees (with Rob Gronkowski and Julian Edelman still very much in the primes of their own careers) and Brady's defense is substantially better than what the Saints will field anytime soon, which will result in more possessions and scoring opportunities. That doesn't mean Brees won't make this a close race. It's just that head coach Bill Belichick has built a well-oiled machine around Brady, one that will keep rolling as long as the quarterback wants to keep playing. Part of being able to break records and post huge career numbers is having a coach who cares about records and stats. Sean Payton will give Drew Brees the opportunity to get the most touchdowns he possibly can. If both Brees and Brady are going into their last game and Brees needs eight touchdown passes, Payton will allow him to throw for nine. That's why I would give the edge to Brees, on top of the fact that he has the skill set. The Patriots have developed a system that no one has caught on to. Even with a destroyed offensive line in 2015, Brady was still able to get the ball out of his hands in two seconds -- so essentially, the pass game is their run game. I look back to what Brady did against the Broncos in the AFC Championship Game. Even though the Patriots lost, Brady threatened to tie the score with a two-point conversion against the best team in football with one healthy offensive lineman. That alone speaks volumes about where he is at 38 years old.
With Brees and Sean Payton, it's always going to be big plays and big yards. The Saints run a true West Coast, progression passing game, but it takes time and a lot of pieces have to be put in place for it to be effective. The longevity of what the Patriots are doing gives Brady the edge, but both of these quarterbacks will play past 40. The Saints throw the ball more than the Patriots do, and Sean Payton is a masterful passing-game coordinator. I think the connection between Payton and Drew Brees is much more dynamic than the one between Bill Belichick and Tom Brady. Belichick doesn't care about throwing the football. He's going to do whatever it takes to win, even if that means running the ball 40 times. The Patriots don't necessarily have to throw the ball to win, while the Saints do. That is why Brees will finish his career with more passing touchdowns. I am going to go with Tom Brady because I think he will be with a better team. A superior team will give him more opportunities to be successful as a QB (and thus, throw more touchdown passes). I know this is not a detailed analysis, but sometimes the simple truth is the best answer.
If you want to make the case for Brees, you could argue he is over a year younger. His defense will not be as good, forcing him to throw the ball more.
But personally, I'm rolling with the better team: Tom Brady's Patriots. Brady is consistently playing at a higher level in the latter part of his career. The way the Patriots' offensive system is set up, coupled with the supporting cast and the way Brady plays the game, it sets him apart even from a guy as good as Brees. Team success also plays a role in this debate, and New England is better right now. Drew Brees is my choice for a number of reasons. First, the New Orleans Saints play eight home games indoors and then at least three more in warm-weather cities in the division. In New England, Tom Brady can face inclement weather late in the season. Also, Brees should get a leg up in that competition this year because, in all probability, Brady will miss some games to suspension. In addition, historically speaking, Saints coach Sean Payton has a tendency to throw the ball more than Patriots coach Bill Belichick, who prefers a more balanced offensive approach. There's also a bit of an age difference: Brees is 37 years old, while Brady will turn 39 before the 2016 season starts.
Brady does have one thing going for him, however, and that is tight end Rob Gronkowski.