Here is a statistical comparison between Chad Henne in his second season (2009) and Tyler Thigpen in his second season (2008). Both played in 14 games. Henne started 13 of 14 while Thigpen started 11 of 14. Here it is:
Touchdowns Henne-12 Thigpen-18
Interceptions Henne-14 Thigpen-12
Completion % Henne-60.8 Thigpen-54.8
Yards Henne-2,878 Thigpen-2,608
Average Yards per Pass Henne-6.4 Thigpen-6.2
Passer Rating Henne-75.2 Thigpen-76.0
Looks very similar, but now factor in rushing statistics as well.
Rush Yards Henne-32 Thigpen-386
Rush TD Henne- 1 Thigpen-3
The big picture points to Thigpen being better than Henne when playing in the same number of games in the same year of their careers. Thigpen's total yards, total touchdowns, and interceptions (2,994 yds, 21 TD, and 12 INT) are better than Henne's (2,910 yds, 13 TD, and 14 INT). In case that wasn't enough to convince you that Thigpen is better than Henne, here's one more fact that's sure to make you a member of the Thiggy fan club: He had that season on a 2-14 Kansas City Chiefs team, while Henne was on a 7-9 Fins squad.
Stats don't lie. The touchdowns and interceptions are the most telling in my opinion. You can't defend Henne by saying that 13 TD to 14 INT is okay because he was only in his second year, when Thigpen had 21 TD and only 12 INT in his second year with a much worse team around him. Thigpen is the better option moving forward. If you had to choose between them as to who is going to be your Franchise QB, these stats prove that it's gotta be Thigpen.