It's not a factor as the Pats like us are fully expecting EJ to play. They already know the Bills are going to run an up tempo offense so that won't change and although we assume the Bills have shown little they have an idea what kind of offense they are going to run as well
The only difference is EJ might run a little more then Tuel which unless he ends up running like crazy similar to Vick in his prime won't impact their gameplan that much