I think its obviously pretty easy to tell the difference between a good QB and a bad one. But differentiating between two great QB's is very difficult, especially since they have unique strengths that makes them great.
I think both Brady and Manning throw great, catchable passes, but I think Manning might be a touch more consistent, its not often you see him just completly whiff a pass, though we do see it every once in a while from Brady.
I think Brady is better with the intangables, Manning often shows his body language and brings his team down as a result if things arent going his way.
One final thing to add, I do not think that you would ever in a million years see Manning dive over the pile like Brady did yesterday.