Between the two games played by NE/NYJ in Weeks 2 and 13, the Patriots went 8-1, beating teams such as the Ravens, the Steelers, the Chargers, and the Colts (though both of those last teams, admittedly, are having down years). The Jets had also gone 8-1 in that time, but aside from the Patriots, they haven't beaten a single team that's .500 or better. The only team they'd even faced during that stretch that does have a record over .500 are the Packers, and they lost that game.
When the Patriots and Jets first met, the Patriots were missing Logan Mankins (Kevin Faulk was New England's leading rusher with 22 yards), still had Randy Moss (who beat an injured Revis for a touchdown), and were dealing with a young and inexperienced defense. The Patriots were a very different team back then. Now, granted, the Jets lost Jim Leonhard just days before the game, so in this second go-around the Jets weren't exactly the same team either.
The Jets aren't as awful as the Patriots made them look last night, but they weren't as good as their record indicated, either. They've had a pretty soft schedule, and a few of those wins were by the skin of their teeth.
I still think both teams are going to make it to the playoffs, though. It'll be interesting to see what happens if they play each other again.