Well yeah. I don't think anyone is dogging the Patriots for having Tom Brady throw the ball 40 times a game, since we've had enough time to realize that that works really well. My understanding is that all these complaints are about playcalling. No matter how good or bad your pass and rush game are individually, running 5-wide, shotgun spreads, and dual-TE constantly does not serve your offensive gameplan at all. It takes away the play action and Brady isn't mobile enough to make defenses pay attention to him.
The Jets game last year was a demonstration of that, as the Jets figured out that they could ignore the run completely, trust their defensive talent to execute the coverage, and let the rest take care of itself. I'm not sure if the Patriots have actually adjusted to that yet.