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One of the more popular ways in which NFL defenses, particularly the Giants, are trying to deal with these freak-of-nature tight ends is with the utilization of a sub package known as "big nickel."
While a nickel defense adapts to the passing game by substituting a linebacker with a cornerback, the "big nickel" takes the concept one step further and removes another linebacker in favor of a safety.
While this certainly makes your defense a bit more susceptible against the run, the Jets have the run-stuffers up front to get the job done themselves with little linebacker support.
The Jets were able to add a multitude of safeties this offseason in LaRon Landry, Yeremiah Bell, Josh Bush and Antonio Allen. As bad as Eric Smith can be in sub packages he can be an effective player.
As Mike Pettine told Brian Costello of the New York Post:
You’ll love Eric Smith at 300 snaps, you don’t like him at 1,000.
While they still don't have their Kerry Rhodes-type that can cover slot receivers and tight ends, they have a better idea of the limitations of their roster, and with a deeper safety group, they can use players to their strengths.