Points for Brees:
-Incredible statistics. It's pretty likely the he ends up number 1 overall in the passing triple crown (yards, TDs, completions).
-Incredible longevity. He's 3rd overall in career weighted AV.
Points against Brees:
-He has a significant statistical advantage due to where he played (San Diego, then in a dome). Compared to his contemporaries (Brady in NE, Rodgers in GB, Manning setting records in Denver), his numbers are rightfully given less credence. Considering his teammates, home-field and era, he's in the most passer friendly environment of all time.
-He's rarely if ever been more than the 3rd best active QB. This happens when you play at the same time as Brady, Manning and Rodgers, as well as a host of other very strong QBs (Roethlisberger, Rivers, Wilson). One all pro appearance in 18 years as a starter is rough.
-0 MVPs. The only other QB selected who didn't win an MVP (other than Baugh and Graham, who played before the award existed) was Staubach.
-Relatively little team success. Just 1 super bowl appearance, 1 super bowl win, 3 conference finals appearances. He missed the playoffs 6 times in his prime, terrible relative to his peers on this list (Brady/Manning have made the playoffs a combined 28 consecutive years, other than 2 missed injury years). He had a lousy defense? Yeah, so did Manning/Brady/Rodgers at times, and those guys still made the playoffs every single season.
Brees vs Manning is a joke. Only the most superficial glance (Brees passing Manning's career records) makes it interesting. 5-0 in terms of MVPs, 7-1 in terms of All-Pro selections. That's it. Brees has made a great career out of playing in a super friendly passing environment, being on teams good enough to win 7-11 games per year, and always being the guy who rounds out the "who are the top 5 QBs playing right now?" question. Manning changed the way the game is played. I'm not a Manning guy, but Brees doesn't belong in the same room.
One real point still in Brees' favor is that he's not done. Neither is Brady but the book on him is basically written - nothing that happens going forward will really impact Brady's legacy one way or the other. It's easy to see Brees winning the SB this year and another SB MVP. If that had happened 12 months earlier does he make the team? Maybe.