Having seen it, I know what you're talking about Marcus. There are subtle hints throughout that sort of piece the plot together for perceptive sorts. Also, I just noticed the use of "button in the eyes" and the "our eyes will be on Coraline" in the song too... crafty lyrics, John.
But yeah, the story was fantastic... it's totally a modern fairytale, without using any of the horribly cliche tropes, like goblins and fairies and trolls and crap. It's a story about kids, and why you can't always get what you want, at least not without a caveat.
Seriously though, the artwork is fantastic... and absolutely EVERYTHING was handcrafted, from the woman who hand-knit all the shirts and pants and clothes on a model scale, the flowers in the garden that moved and lit up... everything. Seeing it using the new Radial Polarization 3D technology is awesome too... it operates on different principles, so it can create all kinds of layers, which actually move as you tilt your head.... I literally found myself craning my head a bit to look around corners in the movie... incredible stuff, and worth the extra ducats.
Oh, and I'm a Michigander, so her dad wearing an MSU sweater, and the Detroit Zoo snowglobe on the mantle won major bonus points.