I can see some inspiration from the Elfen Lied anime. So far as to take the song straight out of there.
I think this plot and the animation are simply based around the song, like the author came up with it while listening to the melody.
Regardless, yeah, this small cartoon is particularly well made in design aspect for 2005, but the plot isn't the best honestly.
Understandable that there was a reason for its' length but making it intentionally short doesn't excuse it at all.