Think about it: Electro from Spiderman, the Emperor from Star Wars, Zuko's sister Princess Azula from the Airbender series all use lightning and are considered almost explicitly to be bad. I'm sure there are other examples as well, these three came to mind. The two other examples are Thor (Marvel) and Pikachu from Pokemon, but Thor is taken from Norse Mythology and Pikachu is a (mouse?) Pokemon. Both Thor and Zeus, two of the main lightning wielders of the past were on the side of good. Why the switch in the modern age?
closed as too broad by Thaddeus Howze♦, Valorum, NikolaiDante, user8719, The Fallen Feb 24 '14 at 23:05
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Summary: Lightning is unpredictable and powerful making it a poor choice for someone who cares about who they target. And bad guys are less likely to care about who they maim.
In classical mythology, Thor and Zeus weren't "good guys". People assumed Thor was protector of Earth because of the violence in the sky, and the fact that the Earth wasn't torn assunder, he must be protecting them.
And, Zeus, he was just as likely to bless you as he was to smite you, turn into a swan and get with your wife.
As for why lightening is considered a "bad" power, firstly look at this photo of lightening generated from the static electricity from a plume of ash in a volcano.
Powerful, and frightening right? There is a reason many people (including me) and animals suffer from Brontophobia - or fear of lightning. One other factor is that lightening is impossible to predict. Because of the fact that lightning is such a chaotic and powerful phenomena explains why many religions revered it.
So as an ability that one can control it is very powerful and very chaotic. You might get your target, you might get the innocent bystander standing near by. If you're a "good" guy, you might care about about who you hurt. If you are the "bad" guy you likely don't care if your caped meddler gets hurt or their plucky sidekick.