Most of my comments on the various story arcs were alternative explanations and interpretations of events, and were meant only to be similar to canon, not actually the same as, since that was the purpose of this thread: how would you change how they were written to make the villains more sympathetic.
As far as characterization goes, while there is less time spent on it in the manga, to me there is more depth to the characters, especially to the good guys. The anime has Usagi maturing less by Stars than she does by the end of R in the manga. The characters are left rather shallow. The backgrounds of the characters gives them a lot more character, to me, though I admit there are elements I really like about the anime, such as Nephrite realizing that he is missing something in the dark kingdom.