No matter where you stand on Kellen Clemens, everybody agrees he did not play particularly well as the starter in 2007. He had a lot working against him from inexperience to a bad offensive line to no running game. People forget another potential key factor. He was running an offense designed for another quarterback. It was a system tailored to Chad Pennington.
Over the past three seasons, Jets fans got sick and tired of hearing the phrase "gamplan specific" to describe the team's offense. What it meant was the system was adaptable. It constantly changed to try and attack the weakness of an opponent. This became irritating because it seemed at times the Jets were more focused on what the other side did poorly than what they did well.
Brian Schottenheimer's system is also adaptable to the players he has. It changed in 2008 after the Jets traded for Brett Favre. The changes were subtle but real. One example is presnap movement. There were lots of players shifting and moving around with Chad Pennington under center. The wily Pennington loved to confuse defenses. This disappeared with Favre. Brett liked to see exactly what was in front of him. This is only one example. Schottenheimer tries to build his offense around his quarterback.
This takes us back to 2007. Clemens took over as the starter midseason. It was too late to make any drastic changes. He more or less had to run an offense designed for Chad Pennington's strengths. Gang Green at least had part of training camp to build a system around Favre. Is this an excuse for Clemens? Not really. A good quarterback should be able to play in any system. Is it another mitigating factor that might explain how the odds were stacked against him? Perhaps.