When all is said and done, you can take all of the regular season stuff and all of the arguments and talk and talk about them, but here is the bottom line:
The Patriots and Colts organizations have both given their all-world quarterbacks great supporting casts and put them in position to win championships many times. Anyone who argues that the Colts are a garbage team without Manning is just stupid. The Colts have lots of terrific players. Dwight Freeney, Robert Mathis, Reggie Wayne, Marvin Harrison, Dallas Clark, Antoine Bethea, just to name a few. The Colts would not be 4-12 without Manning. They've had a top defense several times in the last few years, and they play in a dome, so they should allow (and score) more points. Yes, Brady has had an overall better supporting cast in the big picture, but the gap is not that great.
The results are that Manning has won a single championship, and that was around an all-around underachieving playoff performance that he personally put together in 2006. You can't blame the organization for losses in 2005, 2007, 2008 (when Brady wasn't even playing) 2009, when the Colts had championship caliber defenses and skill players. These were golden opportunities. The "bad supporting cast" argument essentially died after 2004.
Brady has won three championships and put his team in position to win a 4th in 2007, when he played a great game considering the amount of pressure he was facing (makes me laugh to hear Polian complaining about the pass protection last year when Brady was swallowed up on every play.)
I just don't think you can make rational argument that Brady has much better coaching, defenses, or supporting cast anymore. After 2004, the Colts have been better in those categories.