I'm always amazed at how devilishblueyes gets things wrong in new and different ways when it comes to a Brady/Manning discussion.
Brady is the better of the 2. Unlike Manning, Brady has not always had good receivers/weapons. In fact, most of his career, he had average to below average receivers that struggled to make other teams, not "veteran receivers" like someone else said. When Brady filled in for Bledsoe, they weren't "the best, most talented team" either like someone has pointed out. They were 5-11 the year before and were 0-2 when he came in for Bledsoe and oddly enough, their first win was a blowout victory over the Colts that season. Manning's first year with the Colts was with the worst team, but anybody arguing that the Patriots entering Brady's first year as a starter were the best is a complete and total moron.
Players like David Patten, Troy Brown, Deion Branch, David Givens, Bethel Johnson, etc. were not "veteran". Patten was a football journeyman, Brown had been with the team for a decade, Branch, Givens, and Johnson were all draft picks by the Patriots during Brady's time there. None of these player should EVER be confused with Marvin Harrison or Reggie Wayne. Outside of Randy Moss and Chad Ocho Cinco, they have basically never had any "veteran" receivers.
When they faced each other at the early part of the 2000's, the Patriots offense was balanced with run and pass with basically a bunch of marginal players outside of Corey Dillon, who was basically over the hill. Their defense however was good. The Colts and Manning on the other hand, didn't change their offensive philosphy until this past year. Defensively, they were built to play with a lead. Small on defense with great pass rushers.
The difference between the teams was philosphy. The Colts wanted to outscore teams, the Patriots wanted to physically beat them. That changed in 2007 when Brady finally got offensive weapons to match Manning and the Patriots became more reliant on their passing game than anything else.
The difference between the players, is that Brady has played in multiple offensive systems with a revolving door at the skill positions, mainly with marginal talent. Manning on the other hand played in the same system for 12 years, and basically had the same personnel surrounding him for that entire time, not really seeing that change until 2010 when all of those players were either out of the league or hurt.