I think I would take Manning over Brady. Manning epitomizes consistency: 11 consecutive years throwing more than 25 touchdowns (and he already has 24 this year); 11 consecutive years throwing more than 3,500 yards, 9 for over 4,000 (and he already has over 3400 this year). In only his 12th season, Manning has started to pass players like John Elway on the all-time lists. His main fault is that he's averaged almost 15 interceptions a year, though that number is inflated by his horrendous rookie campaign.
With Manning at the helm, the Colts have had 10 seasons with 10 or more victories, including the past 8 consecutive, not to mention 6 consecutive seasons with 12 or more victories -- and they already have 11 again this year. The Colts have amassed an impressive string of undefeated streaks, starting out 5-0 in 2003; 13-0 in 2005; 9-0 in 2006; 7-0 in 2007; and now 11-0 in 2009.
Other than that, I can't quibble with your list. Excellent post.