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I don't think the Alliance is as bad as he thinks it, nor is the freedom of the outer worlds better (not only do they lack the tech, but they tend to be run by local tyrants worse than the Alliance), but I still think of Mal as better than many, and more well meaning than he himself realizes.
I see good and bad guys on both sides of the law, both in his Verse, and in the real world.
I think hat Mal is supposed to be the classic antihero, the guy who generally does the right thing, though not always for the right reasons, but also doesn't get all broken hearted when he does something bad. Visualize Deadpool with a space ship.
Mal was well adapted to his world. Guided by his own sense of justice rather than the collective control. I love his individuality and strength, and his desire for all to see truth and make their own choices.