How the formation is best defended is dependent upon your scheme and personnel. Obviously, it is going to be played with your base run defense set. Then, you need to look at the design of the plays. For the most part, Miami's version of the Wildcat is heavily Triple Option. Granted, there isn't the option of the pitch to the wingback, but it is essentially a Triple Option in effect. So, what does that entail? You need to defend the A gap as well as the C/D gap. One of the advantages of the Triple Option is that the potential fullback handoff (or in this case, QB dive) holds the inside linebackers long enough to allow the play to develop to the outside. If the pursuit doesn't arrive in time, the wingback is in a footrace with the safety to the pylon.
In Cowher's case, his defense is a 1-gap 34 predicated upon penetration. It's almost a 33 stack in execution. This is why his breakdown involved the disruption of the mesh point. The problem with this is that penetration against such an offense is a big play defense. It's either a TFL, a 1st or in many cases; hash, numbers, sideline, six. It's a different defense than what the Pats run.
In the case of NE, when they effectively defended the set in the rematch, it was about keeping the play contained. The defense still wasn't stellar in pursuit from the playside backer (MIA targeted Bruschi for obvious reasons) an because of this, responsibility laid with the 5 tech's and the OLB's. I spent some time watching the DVR of the game and found out how it was defensed. On the plays where the formation was stopped, Wilfork dominated and pushed Satelle upfield taking away the angle for the A gaps (negating the QB dive). Because of this interior domination, the ILB's were free to pursue. Seymour and Warren retained outside leverage on the tackles and sealed the edges. The OLB's and playside ILB were able to mop up with the help of the crashing safety.
When the offense was successful, the tackles won the matchup with the 5-techs. While this was key in opening the gaps, the real key to the play was the blocking scheme. I noticed just how much lineman movement was going on in these plays. Nearly every play, both guards pulled to kick out the OLB and pickup any crashing flack. This was accompanied by a cracking TE trying to seal Mayo. Interestingly, the scheme was designed to seal Mayo, kick out the OLB, and pause Bruschi with the pulls. From the earliest stages of football, ILB's are taught to read the action of the guards. Brickhead LB coaches like the mantra "where the guard goes, you follow". It's effective through highschool, but less so in college where the speed of the game increases enough to exploit this read. That's why there are many plays where the flow of the guards are to the backside of the play. Bruschi is obviously one of the most aware defenders in football, so this concept wasn't very sound. That said, it was designed to exploit Bruschi's lack of speed. The crack was designed to seal Mayo, who they obviously viewed as the key to the flow. On nearly every play, there was a blocker assigned to seal or disrupt the pursuit of Mayo. This was not the case with Bruschi.
So, what did I learn in watching this? That the key to the defense was reliant upon every normal principal they harp on. Maintain gap integrity, control the LOS, turn the play inside, and mop up with the flow of the will or crashing backside safety. The other interesting note is that on nearly every play, the backside safety was coming hard. With Pat White in the mix, this assignment will no longer be a viable one. Bringing the backside safety with a legit thrower rolling to the backside will be suicide. It would be too easy for the play to conceal the TE route. It could start with the look of a designed crack from the playside TE, and have him release into the zone vacated by the safety. This would sell out the run read of the defense and make the play wide open. As the formation and personnel evolve, so will the ways to defend it. With every permutation, there will have to be an added wrinkle. However, the basics have been established. It's going to be an interesting AFCE story line to follow this season with White now in Miami.