Brady is a coach to a certain extent. He coaches his receivers to know that they are running a planned route to a certain point, and then they need to modify the route depending on where the nearest defender is because he's going to throw the ball to the location away from that defender, not necessarily where the route was planned. He's not usually throwing the ball to a pre-planned spot on the field, but rather to the spot the defense gives him and his receivers have to learn that to work well with him. Manning used to do that to a lesser extent because he wasn't as good (no one else is even close) at assessing the defense before the snap. Sometimes he (Brady) makes that read before the snap and changes the play so the receiver knows at the snap, sometimes he needs a second or two to read the play in progress. In essence, he checks down receivers before the snap and so schemes don't work well against him.
Great overall defenses like the historical ones at Seattle, Baltimore, and NY Giants that could give tight man-to-man right off the snap are required to reduce his effectiveness. Or, if his protection is compromised, the defense can afford to make the back end coverage a little more complicated and confound his ability to make the reads a little more.