OP: Incomplete analysis of in-zone defense.
Layered defenses in both the NZ and DZ (more so NZ, but still...) survive on their ability to create turnovers and utilize transition to their advantage. They structure their defense to force turnovers and then when they retrieve the turnover they are NOT going into a structured defense on the other side. Less quantity, more quality.
One pertinent way to beat it (and many coaches know this, to say that no one has ever thought of a way to beat it would imply the New York Rangers have won four straight Stanley Cups) is to sustain attack time. Shooting into today's shin pads is a recipe for odd-man chances against, it doesn't answer the real problem at hand: the ability to generate scoring chances via sustained attack time.
We attacked on the rush. 2 on 3, 2 on 4, 1 on 3, 3 on 5, out-numbered at every pass. Out-numbered out high. Out-numbered going to the net. Out-numbered going the other way. We thought (evidently) we could catch them by surprise - we didn't. And, in conjunction, thought we could overwhelm with talent - we couldn't.
The advantage belongs to the defense in most even-numbered situations. So, you can only imagine what kind of disadvantage there is when out-numbered. See: rarity of shorthanded goals.
The shift of NZ defenses back to their own zone was brought about, in part, by the elimination of the red line and the proliferation of goaltending (and equipment). The same principles apply on how you can beat it however.
They are structured in front of the net to force shots away from the "house" which encompasses the slot but without necessarily guarding it directly. Pucks should be put into selected corners promote a positive matchup (i.e. Torey Krug's corner for Chris Kunitz forecheck/retrieval). The center should support on the "net side" of the corner battle. The off wing should offer weak side support or net-front/slot presence - prevent the defenseman from getting cleanly involved in the defensive support/retrieval. If we're in the LW corner, we should have a LHS d-man on the left point. Weak side defenseman should read the play and either hold the middle of the ice or shade slightly outside the zone if the puck has a less than 50% chance of being retained (adjust percentage to your own personal coaching style and game elements). Establish a four-man cycle utilizing a strong side defenseman.
Manufacture offense from behind the net, get eyes turned away from you and then you'll be able to quick strike the front of the net. The utilization of the cycle helps to pull defensive players from their positioning and create better matchups at better places on the ice (i.e. a wing defending the front of the net, etc.). The defense is layered, pull the layers apart and begin to attack from within.
The wear of longer, harder shifts will reap their rewards later in the game. Defensive shifts are usually tougher than offensive ones (see: shift length on PK vs. PP). Having to defend for 75 seconds will wear down nearly all players.
Unfortunately, the only good forechecking/board players/cyclers forwards we have are: Crosby, Dupuis, Kunitz, Iginla, Neal (kinda), Kennedy, Morrow, Cooke, Sutter, Vitale, Adams, Glass, but very few others...so you can see how we would be at a disadvantage to utilize this systemic adjustment. This is my serious face.