I agree with you that BB did not plan it to go the way it did. What I don't like is that BB didn't ADJUST to help his Defense after seeing what was happening.
I'm one of the biggest proponents of getting the running game involved in the offense on this board. I also hold your opinion in high regard. But I'm afraid that I have to respectfully disagree in this instance.
Kontra has respectfully summed things up fairly well. If the Pats had gone run-heavy and lost against a team with a terrific run D and a lousy pass D, behind a crippled OL and having lost their best bell-cow back, everyone would be in an uproar.
The Jets had a game plan too, and it was a good one: run the ball against a defense missing their defensive signal caller, let Geno Smith use his legs, and don't ask him to do too much. The executed that game plan very well, to their credit, not turning the ball over once against a team tied for the league lead in turnovers. Give them credit for that.
The Pats never led by more than 8 points, so it's hard to see them converting to a rushing attack to chew up the clock. Sure, I would have loved to see something like the 2012 Miami game where we ran the ball down their throat in the 4th quarter, but I don't think that was likely to happen given our OL and their DL. The Jets didn't punt until 4 minutes left in the 3rd quarter, they didn't turn the ball over, the Pats had lousy field position (their best starting field position on their first 7 drives was their own 30), and they couldn't get enough separation or good enough field position to trust their running game to chew up the clock.
When exactly do you think that we should have used the running game to chew up the clock? Our defense couldn't get them off the field in the first half, and they scored 4 FGs, then chewed up 6 minutes of clock time to start the second half while scoring a TD to take a 19-17 lead. We moved the ball well enough to score a FG and retake the lead on our next drive (starting from our 29), then forced a punt and started from our own 13 with a 1 point lead. Is that where we should have protected the lead and conserved time by running the ball more? We went 3 and out on that drive with one run (a 6 yard carry by Vereen). The drive had 2 incompletions, one a drop by Gronk. The next drive also went 3 and out, with a drop by Edelman. The drops (by our 2 most reliable receivers) IMO were key - they weren't turnovers, but they might as well have been, killing drives and taking time off the clock. That wasn't scheme - that was poor execution.
The only time that I saw BB really in a position to trust the running game to take time of the clock, he did - during the last drive.
I think this close win was a combination of good game planning and execution by the Jets, poor defensive play in Mayo's absence, and poor execution by Brady's receivers. Better execution, and this game would not have been as close. I'm just not sure where the "adjustments" were to be made. Again, if the Pats had gone run-heavy and lost, they would have been justifiably lambasted for poor strategy.