Maybe I'm not understanding you, but are you saying Brady had less weapons than Manning?
This is absolutely true over the course of their careers though. People forget that Brady had a pretty average offense until 2007. Troy Brown was the best receiver, and then you had guys like Deion Branch, David Patten, Ben Watson, Daniel Graham, Antoine Smith, etc. The only great offensive player he really had other than Brown was Corey Dillon in 04. In Indy, Manning had Marvin Harrison, Reggie Wayne, Dallas Clark who were all great players, and then Edgerrin James who was pretty good.