If the question is: Would I rather have Brady or Manning?
The answer is simple. It's Brady, every day of the week. In the end Brady is just a calmer personality. Manning can get frustrated pretty easily, and that hurts him. Particularly in big games. This was on display against the Redskins. After getting stupidly angry after the failed slant on the goal line, he came out and threw an interception almost right away. You just don't see that very often from Brady.
That said, Manning is an amazing QB. So if we're talking the offense as a whole? There is simply no question. The Broncos are better at nearly every position, save one of the tight-ends..and it's not a huge gulf between Gronk and Thomas.