1) Brady didn't throw high. With the Cowboys sitting over the top of the receivers, Brady made sure he was going to throw the ball into the dirt instead of over his receivers. He threw two short of the receiver, tossed another away, and then had two batted at the line (although one could've been taken to the house). One of his lone deep shots (to Matthew Slater) was far wide out of bounds. This is very intentional quarterbacking from Brady and he kept to his game plan.
2) He and Amendola just aren't meshing. Whenever Amendola rolls into the flat, Brady seems to throw it down by his feet, behind him, or just a hair too far ahead of him. Over the season, I just have one strike in five passes to the short left to Amendola. Edelman had eight strikes out of 13 passes. Conversely, Amendola is a perfect four for four in the short middle, so the Patriots might think about sending him on shallow crosser a little more if they want to get him involved.
3) Brady is absolute money in the 10-20 region this season, but he had his first two misfires against Cowboys in this region. Those two balls short of the receivers game to the right side of the field to Rob Gronkowski and Dion Lewis, where the tight coverage led to Brady throwing the ball where his receivers never had a chance to make a play. But in the 10-20 range towards the left or the middle is amazing. Brady has 12 bullseyes on 14 attempts, with the two misses still within the strike zone.
4) The pressure seemed to get to Brady as his dump off passes behind the line of scrimmage were slightly off target. Not only did Lewis have to make a great catch on his touchdown scamper, Brady was throwing away from the player's momentum time and time again, even if there wasn't a defender by the receiver. This is the result of hurried passes, and the Patriots ability to move the chains hinged upon the fact that short passes have slightly more room for error.
5) Brady seems to be very comfortable in all regions short of the 20+ yard marker. He really has the ability to move the ball in any of these locations, with his worst section actually towards the left behind the line of scrimmage. He has 7 bullseyes on 12 attempts, and four passes that were slightly off target. When your weakest range is behind the line of scrimmage, your quarterback is in a really interesting place.