I'd still take Manning over Brady. Brady would be #2, Warner #3 (although he has an odd career), and Rothlisberger #4.
I left Favre out of my evaluation, simply because his latter career has overall been distinguishable from his earlier, greater years.
The only thing Manning did better than Brady was make better commercials.
He threw for more yards in a video gamish sort of way, but that's it. That's all he's got. I think he might have an extra MVP award.
Brady did more with less and isn't personally responsible for any Super Bowl losses like Manning.
More rings against better opponents and his SB loss was in the last minute and half, which took a miracle play and he wasn't personally responsible for it.
Also played with virtually no Pro Bowlers on offense till after his rings, unlike Manning who had HOFers
The only advantage Brady had was Adam V