Another point I forgot to mention, in my list of virtues, was the depiction of a truly Lawful Evil character.
Notice how lawful, even in defeat, no cheap shots, fully cognizent of his role and part in the universe ("I am a monster. There is no place for me in the new world, any more than there is for you ...") and content with it.
Also the captain "Mal" was drawn well, as the "reluctant hero" type, though there were subtle degrees of reluctancy and heroism, cf. Jane, for example.
It was a good SF film because the SF didn't get in the way of the story; a facilitator, it was merely there to help explore some other (always) more interesting sociological commentary.
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I agree, the Operative was very Lawful Evil