Well, Bill Cipher's sad story might be that he is a being of pure chaos. He has no moral compass in the traditional sense. However, this lack of a normal moral or emotional framework could be seen as his tragedy. He doesn't experience the world in the same way as the other characters. He might be envious of the relationships and emotions that the normal inhabitants of Gravity Falls have. He can manipulate and control, but he can't truly feel the warmth of friendship or love. His actions are driven by his chaotic nature rather than positive emotions, and that could be considered a sad state of being.
In the Bill Cipher story, his sad part could be that he is trapped in his own nature. He is a symbol of pure chaos. Despite his power, he can't escape his role. He is feared and hated by most characters in the Gravity Falls universe. This isolation from the rest of the world, being the outcast, is a form of sadness. He may long for something more than just destruction, but his form and the nature of his power don't allow him to have a normal relationship or a peaceful existence.