I agree, that in Star Wars, the good and bad side seem to be abitrary. I feel its fundamental message is that “whoever’s side your’e on is the good one”- kind of like the Americans assuming the Russians were all bad.
Manicheaism is best understood as an etiology of moral and non-moral evil. It is not an ‘equal’ dualism- of which, indeed, I cannot think of any examples, even in Zoroastrianism. “The Father of Greatness” is the first and eternal God- but evil is held to exist independently of “The Father of Greatness”.
If you think about it, the meontological explanation of evil (that evil is really non-existence, and therefore not created by God) really points to the same reality- which is to say, the experience of ‘good’ and ‘bad’ as opposing forces- moral dualism.
Star Wars reduces this moral dualism to something abitrary- to black uniforms versus blonde hair- to physical ugliness versus physical beauty.