Bottle Fairy (anime)/WMG

The series is a St Elsewhere-style Mind Screw.
Steven den Beste has a bizarre theory about what's going on in this show:

This show is about the crazy little sister of our long-suffering male protagonist. The fairies are toy fairies that come in bottles; but she believes that she is the fairies, and the series is largely from her POV, so she is filmed as she sees herself - as the fairies. We only get to see her as she truly is in the last episode.

This is very unlikely to be what the writers were thinking, but it makes a twisted kind of sense. Still, if you read the long form - it's kind of depressing.