Suppose every Patriots WR were 6' 4", with great speed and leaping ability, but (to make them affordable) nothing special in the quick-cut getting open area. Then an offense that simply sent them all running downfield would be very hard to stop, because no team has enough DBs skilled enough to cover guys like that, even if they indeed have 1 or 2.
So what do you do against a team like that? You commit to the rush, trying to get to the QB before those guys get open. That otherwise unstoppable attack does have an Achilles heel.
Well, the Pats had an offense brimming with guys who could beat coverage in the middle of the field, some of them (against most defenses) getting open quickly. It was almost unstoppable. But Ryan found the Achilles heel of the scheme.
Only in this case, I don't think the Achilles heel is NECESSARILY crippling. Guys WERE open -- they just weren't open in ways Brady could recognize, or make ideal throws to, or they were the wrong guys (Crumpler, no longer the most reliable of receivers). That can all, I'm guessing, be counterschemed against.