There are a few things that'll make you go "Holy shit!" on a second viewing of the film, such as the fact that Edward's lip movements really do seem unnatural, and he really does look dead, rather than ill. There's also the fact that he doesn't blink, ever, and is wearing the same suit throughout the entire film.
If you watch it again, you also realize that in every single shot in which Edward is talking, Ella's hand is always behind his back.
All the dummies fall into the Uncanny Valley. Mary Shaw was obsessed with making "the perfect doll;" the creepiness of her dummies stems from her not getting it quite right. It also explains why she had so many, and why Ella is completely human-looking; Shaw finally perfected her doll-making.
Mary Shaw wishes to eliminate the families of those who murdered her; considering how she always wanted a family of her own, she probably sees this as the worst possible thing to happen to someone.
Mary Shaw knew who Henry and Michael were; considering how she always wanted children (the treatment of her dummies and the doll Jamie finds in the abandoned theatre prove this), it's not hard to think that she was stalking the children of Raven's Fair.
Why do the cops let Jamie keep the dummy and trunk? If they think he killed Lisa, they should have wanted to prove that Jamie mailed the stuff to himself. Not only do they let him keep them, the cops leave them at the crime scene so they didn't even thoroughly examine them. Indeed it takes ten seconds of examination for Jamie to find evidence that the trunk originated from his hometown.