ESPN has a Rodgers v Brady page with Ashley Fox arguing for Rodgers and John Clayton arguing for Brady.

http://espn.go.com/nfl/hot?id=7119249

Here's my breakdown.  I'll give Brady a slight edge at pre-snap reads, only for his experience.  It's very difficult to determine how well a QB makes a pre-snap read.  I'll rate them equal at post-snap reads, which are easier to determine.  How many bad throws does a QB make into coverage?  Neither Brady nor Rodgers make mistakes after the play starts.

In the pocket, I'd rate Brady and Rodgers equal.  Both are highly accurate; Rodgers probably has a bit more zip on the ball.  The big difference, however, is mobility and movement outside of the pocket.  Brady has little speed and doesn't operate much out of the pocket from games I've seen.  Rodgers may be the best in the league at breaking the pocket and making consistent downfield throws while on the move. 

That mobility element makes Rodgers number one in my book with Brady a close second. 

Clayton misses on a couple of arguments.  First, he says that Brady has more rings.  I'd point out that all those rings were captured before Rodgers entered the league.  I can pick an arbitrary time frame also; let's say the past three seasons that Rodgers has been a starter.  Aaron has more rings and playoff victories in that time frame than Brady.

Clayton also references game winning drives.  That's the biggest canard in rating QBs.  Only the vaguest definition exists for game winning drives.  Brady is to be applauded for leading the Patriots to a late victory over the Cowboys.  By the same token, Rodgers is one win away from tying the NFL record for most consecutive games never trailing or tied in the fourth quarter.  Hard to come from behind when you're never behind.  Rodgers should receive equal credit for getting his team into the lead early and maintaining it. 

Either quarterback can lead a team to a championship.  If the argument is who is the best quarterback NOW, the nod goes to Rodgers, the best player in the NFL.