Well, the Pats could run the ball, but there was a cost involved.
Just to be clear, I think BGE is a fine, straight-ahead, one-cut runner with very good vision for the developing hole and the decisiveness to hit it with good timing. He runs squared up, with very good pad-level and better than average low-gear power, and he plays with exceptional ball-security. In short, a near perfect between the tackles guy.
However, he doesn't have the speed to get around the end more than once in awhile. He doesn't really have a second cut to escape the LB level or the extra gear to do much when he does escape. Most important, he doesn't get very deep into the LB level without a dedicated blocker - a TE (Crumpler, mostly) or a FB (Morris).
And that's the cost. In order for BGE to run effectively with any consistency, the Pats have to take one of their more effective pass-catchers off the field. Because the Jets, with their strong D-line, knew that the Pats couldn't run effectively with any consistency out of, say, a 4-WR/1-RB set, they could afford to keep 7-8 guys in coverage (5-6 of them between the numbers in the short/intermediate areas where virtually all of our pass-catchers do their best work). When the Pats took a pass-catcher off the field for the extra blocker, the Jets simply cheated up with a safety and/or LB and could afford to do so since there was at least one less target to cover.
In short, without a between the tackles RB who is a legit threat to break off several good runs on his own even without extra blocking help, and without any pass-catchers who can work the sidelines and deep zones effectively with any consistency, the Pats offense can be thoroughly stymied by a well-executed defense that has decent coverage LBs.
