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I'm not saying they should've gone down to earth and represent the Gods as they were in Greek Mythos cause there's no way in the world they can depict the actions of Zeus (or any of the other Gods) as Child Friendly. But I found that, and this extends to more than just this movie, that Hades, or any form of a death god or god of the underworld are often depicted as evil despite them not being so in the original mythos.
In the case of Disney's Heracles Hercules, wouldn't it have made more sense for Zeus to be the bad guy? or if not antagonist, he'd be a "bad father" with Hera being the evil step mother who doesn't approve of Heracles. Y'know, like most evil Disney Step-mothers.
Hades didn't really do much of anything to warrant being treated to this extreme of an evil character. Even his personality was a massive switch up. Disney's Hades was very bombastic, loud, charismatic, sassy, and somewhat flamboyant, something his original Greek counterpart didn't display much of.
The only real reason I can think of now is that since America, or Disney is a highly Christian or Catholic based country (I still don't know how to distinguish the two), they wanted to portray the God of the underworld as evil since it's easier to align with someone like Satan or the Devil. Or at least it'd be a hard sell to parents to depict the greater Gods above as evil. As for the personality, it's just easier to get kids to be invested in him as a villain since he is so fun to watch.