A couple of misconceptions that just won't die:
There's the lazy, simplistic "count the rings" argument. While that does work for determining the best teams, and the age of a tree, it's no way to objectively compare QB play. Counting the rings puts Plunkett ahead of Warner ahead of Marino. Not that Bradshaw didn't eventually turn into a great player, but his team had already won two championships before he started to appear among the top 10 passers with any consistency. Until that happened, the Steelers won with defense, often winning despite Bradshaw.
The other misconception is to think you can compare individual statistics across eras. If that's true, then Sam Bradford (79.3) is better than Unitas (78.2), even though Unitas led the league three times and was top 5 eleven times. Look at this list of the top 5 passers of 1978:
1. Staubach 84.9
2. Bradshaw 84.7
3. Fouts 83.0
4. Griese 82.4
5. A. Manning 81.7
Most of those ratings would not have been in the top 20 in 2013. When comparing across eras, you have to ignore the rating and look at the ranking.
If you still want to use the rating, you can adjust the rating for era. Using WPB's list from the OP, here's the percentage difference between these QB's ratings and the average rating of the years they played.
10 - Andrew Luck -3.0% (10)
9 - John Brodie +9.9% (6)
8 - Randall Cunningham +8.7% (7)
7 - Ken Stabler +10.6% (5)
6 - Aaron Rodgers +21.3% (2)
5 - Roger Staubach +27.6% (1)
4 - Jim Kelly +10.9% (4)
3 - Joe Namath +7.5% (8)
2 - Terry Bradshaw +5.2% (9)
1 - Tom Brady +16.0% (3)
Not even on the list: Griese +17.7%. To me, that percentage and the ranking in parentheses comes closer to being a real list of the best #12's, and not some historically ignorant waste of everyone's time.
As for non-#12's, Romo is +14.6%. Aikman was +5.8% over his career, but +17.2% from 1991-95. And here's the all-time top 5, regardless of jersey number:
1. Otto Graham +38.8%
2. Roger Staubach +27.6%
3. Steve Young +25.7%
4. Len Dawson +25.3%
5. Sonny Jurgensen +25.0%