I think there are few things to note regarding how I use layering now compared to my old style. First of all, the Application layer isn't mandatory; it is only there if it really adds value. Since my Domain layer is so much richer than before, it's often not interesting with the Application layer.
Another difference is that instead of all calls going down, the Infrastructure layer might "know" about the Domain layer and might create instances there when reconstituting from persistence. The point is that the Domain Model should be oblivious of the infrastructure.