Board Thread:Theories and Speculation/@comment-1872728-20151019025302/@comment-1872728-20151024111359

In conclusion:

Naruto World: Susanoo's colour is based on the user's chakra colour. Susanoo's appearance is based on the user's appearance as well.

Real World: "Good-guy-bright-bad-guy-dark" cliches, and different colours of the rainbow to differentiate them.