You'd be hard pressed to prove Brady never had great numbers in the past.
In 2005 Brady led the league in passing yards, 3rd in touchdowns, 6th in passer rating.
In 2004 Brady was 10th in yards, 6th in touchdowns and 9th in passer rating.
In 2003 Brady was 6th in passing yards, tied for 7th in touchdowns, 10th in passer rating.
In 2002 Brady was 6th in passing yards, 1st in touchdowns and 9th in passer rating.
This year, Manning is 5th in passing yards, 6th in touchdowns and 8th in passer rating through 11 games.
Without a standout reciever (harriosn did play 5 games this year), Manning's stats this year are very comparable to Brady's career when he had no standout reciever.
However, compare Brady's stats this year, now when he has weapons, to Mannings career when he had Harrison and Wayne.
As far as the running game and defense winning it for the Pats, from 2001-2006 the colts gained more rushing yards then the Pats 4 out of 6 years. Going by points allowed, the Pats allowed fewer points per game 4 out of 6 years. It would be my opinion that the rushing and defense arguement washes.
Who would I like more on my team? Both are outstanding talents who will likely have HoF careers. Brady would be my pick, for the reason I think he'll have more championships then Manning will, and championship wins are why they play the game. If the roles where reversed and Manning won more Suber bowls, I'd take him.