I'd be surpised if Smith is the 3rd string QB because I don't think the Jets are going to hand the backup job to Clemens. I think they want a veteran to challenge Clemens for the backup job. I also think they are committed to Smith as a WR and don't want him to have to worry about QB too.
I think that being the type of player Smith is and how competitive he seems he will study the QB's plays as well waiting for his big day in the sun. Also i think being a Wide Receiver in the nfl you have to know what the other wide receivers are doing as well you should know everybodys route. so since he has the QB state of mind he is already on top of his game.
I definitely hold my breath when he gets hit, but the odds of losing 2 QB's in one game is pretty low. I think it's a fairly safe bet to rely on Smith as an emergency 3rd string QB if Penny and Clemens went down. If that were the case, we would surely be picking up someone on the waiver wire the following week. I guess we just see it differently.
