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That's honestly part of what sold me on Chrysalis; the fact that she kept her evilness under wraps long enough to no only fool Celestia and Shining Armor, but the audience as well. You couldn't tell whether she was being evil or just a bitch; you knew
something was wrong, but you didn't know what. It raised the tension a lot more than if it would have been obvious from the start what was going on. You don't get that kind of ambiguity in kids' show villains very often. The other thing I liked about Chrysalis was that she was a threat primarily because of her planning rather than her sheer power level. NMM and Discord were straight up threats simply because they were powerful. Chrysalis had to beguile her way into Canterlot before attempting a direct attack. She showed far more forethought than Discord or NMM, and she had more of a personality than Sombra did.
That said, I still think Discord was the best villain in terms of writing and personality, but Chrysalis is definitely up there.
As for whether she was evil, I think that stranding a bride in a cave on her wedding day, taking her place, and then brainwashing the groom to use as a power source is pretty evil. Just because we don't realize that she was doing that until late in the episode doesn't mean that she wasn't.
edited 3rd Jan '13 11:27:12 AM by JapaneseTeeth