Since the title of this thread suggests the Eli/Brady comparison as much as anything else I really think the interesting thing to watch going forward is still the rules changes and the impact they have had on the quarterback position.
I still think what bears watching is what appears to me to be a change in the basic elements of the quarterback position. I think that where a quarterback's game management skills, those of Brady and Payton for example were much admired I think those elements of quarterback play are less important in this era. I would still not trade Brady or even a healthy Payton for Eli and I still think Tom is the best quarterback in football.
Looking for a moment at big play capability, which everybody acknowledges is the difference in the NFL, and then overlaying quarterback play on that what do we see over time with these gradual rule changes.
If we go back to the 50's and 60's the spectacular, big plays were for the most part from the running back position followed by receiver. The quarterback was the consummate game manager.
Through the 70's and 80's running backs began to fade a bit from the perspective of big play potential and on the offensive side of the ball receivers came to the front and we had the era of big spectacular plays coming from the defense. We even had defenders vying for MVP honors.
In the late 80's and 90's spectacular plays from receivers catching the ball and defenders either making plays all over the field or defenders that could control the line of scrimmage and rush the passer where the spectacular, big play guys.
That era lasted into the mid-2000's.
Now plays by defenders out in the field are almost impossible by virtue of the rules changes. Receivers are capable of making big plays but the spectacular plays seem for the most part reserved for the quarterback position and those defenders trying to disrupt the quarterback.
A quarterback's ability to game manage, the real strength of the Tom's and Payton's is surely less vital than it once was. Instead quarterbacks have been put into position where they now have the capability to make big plays by virtue of their physicality. Some of them can make big plays with their legs taking advantage in part of how well protected they are by the rules. Some can make big spectacular plays with their arms again in part because they are so well protected by the rules and some can do both.
Look at the pass to Manningham at the end of the SB. I mentioned this earlier in a different context but that pass has become the benchmark by which passers are now rated. That is a very physically demanding pass. One that I do not think either Tom or Payton is capable of making. That pass has to be thrown about 40 yards down-field, and along the sideline and in a window about 1' square. It must be thrown with enough juice on the ball so that it does not tail off or decelerate at the end as it must lead the receiver away from both the corner and the safety trying to get over the top of the play.
Folks that have called Manningham's catch great have got it wrong in my view. Eli's pass was exceptional and in fact spectacular.
So the real question to me is that given the rules we have now, will quarterback play continue to evolve such that big physically demanding spectacular plays like those Cam Newton and Eli are capable of making become the norm for the next era of "great" quarterbacks. Seems to me that Brady and Payton are examples of the last generation of quarterbacks. Rogers, Brees and maybe Smith and Rivers sit squarely on the dividing line. Guys like Eli, Newton, Vick sit on the other side of that line. They are less consistent by and large, not as good at game management but more capable with regard to the spectacular play.
The one constant in all of this is the importance of the big, spectacular play in pro football. The difference in my view is that guys like Eli and Cam are as capable in that regard as the LT's, Prime Times, Rice and Irvin and the Gale Sayers and Jim Brown's of past generations.
Now if the game can be kept close, a whole game's worth of inconsistent quarterback play devoid of noticeable game management superiority can be completely upset by a couple of great, spectacular plays from the quarterback position.