There are spoilers below.
I just really appreciated The Leftovers for its execution. I mean, as far as acting, directing, and score goes, that show fucking killed it, in my opinion. The camera shot of Wayne when he died just drove into my brain and stuck there like a nail. Fucking horrifying.
The use of the wax doubles was horrifying not for what it recalled, since as viewers we can only sympathize with the characters (none of us have had our loved ones literally disappear into thin air, so we can't empathize), but because of the uncanny quality of their appearance. I won't begin to imagine how the Guilty Remnant managed to sneak quietly into everyone's homes and successfully plant these doppelgangers (that would ruin the fun), but the placement of this episode was perfect because it immediately followed the episode in which we get to witness several perspectives of the original event. We were thus all familiar with the positions in which many of these doppelgangers would appear, and who they were meant to represent.
The ironic quality of the final episode was that it backfired. The Guilty Remnant didn't succeed in making people remember; or rather, it only forced people to remember momentarily. By the close of the episode, I think we're meant to realize that people are, in fact, able to move on even more easily. And perhaps, in fact, that was actually the secret motive of the Remnant all along...
The replacement of the doppelgangers in the finale recalls the psychoanalytic notion of trauma: an inability to reconcile the unexpectedness of a particularly traumatic event which thus leaves an unsuturable wound in the subject. These subjects then suffer from various psychic symptoms, such as nightmares or neurotic behavior, because their bodies and minds are trying to "heal" the traumatic wound, so to speak. The replacement of the doppelgangers may actually have served as a kind of medicinal healing to the trauma of the original event. People may not have been expecting it, but they had a referent for it; it fit into a kind of socio-symbolic framework, they understand the act even if they didn't understand the original vanishing. I don't mean that they understand why the Remnant did it, but merely that the appearance of the dummies fits a pattern. Imagine if the original event had never happened - in that case, waking up to find false dummies in your kitchen would be a traumatic experience in its own right. In the case of the show, however, it may have still been traumatic, but it makes a certain kind of sense - those doppelgangers fill a space, if only briefly, that needs to be filled.
Their presence means something, whereas the original disappearance doesn't mean anything.