Astrobot,
First, good thinking. I think YPA is a way underrated statistic and is a very good way to measure a quarterback's performance.
I think your analysis largely depends on whether it is fair to consider this JP's first year. It is his third in the league, and he did have eight starts before this season. By comparison, Kerry Collins' season that you list was his first - and his franchise's first as well. By his second year, he was a Pro Bowler.
Also, it doesn't make much sense to compare JP to quarterbacks of previous eras. Statistics were just too different then.