They have weaknesses, sure. They could have lost if things had gone a little differently, sure. You can say the same for just about any game between two above average teams (I still think the Falcons are above average at least).
The fact is the Pats are 4-0. Brady is making less mistakes, the defense is holding in the red zone consistently, and the team is playing the brand of smart football that has led them to success (during the season, anyway) for over a decade. Every team has weaknesses, every team has personnel issues, but the Pats almost always find a way to win in spite of that stuff (again, during the regular season at least).
Soon Gronk will be back which will make the offense better. Thompkins will continue to improve and develop chemistry with Brady. Amendola might get reconstructive surgery to turn his bones into gorilla glass and actually play a few more games.
I'm not saying the Pats are world-beaters and your points are definitely sound (particularly on Wilfork) but I can't see them winning less than 11 or 12 games. And as much as I'm loving the Dolphins so far this season like I said earlier I think they are overachieving somewhat at the moment and I think their youth, inexperience, and lack of depth will end up costing them at least a few games.
Right now with the way things are shaping up I just can't see anyone but New England winning the division.