I asked this because I've watched two great videos regarding what makes a good Sonic villain:

Both from SONICSTA. He's a great guy and a great video maker. You can check out his channel if you want.

But what aspects do you think make a great MLP villain and why?

What's your question exactly? Are you asking: "Which of the villains we've been shown are great and why?" or "What WOULD make a great MLP villain?"

As far as villains we've been shown, Discord probably takes the cake (as much as I want to put Sombra as the No 1 MLP villain I can recognize he was a wasted potential) in this aspect. He was the cheesy, over the top and unhinged freak while he was starring as MLP's main villain. But he wasn't just some psycho that wanted to destroy all of Equestria. He was a perfect representation of the 'irrepressible individual' who gives Equestria's established morals the middle finger and just does as he likes, abusing his own powers with no regard for others' safety. Above all else tho, the guy was entertaining as hell. There are few characters that demand the audience's attention like Discord does. You could probably star him as the main character and the show would still be good.

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"What WOULD make a great MLP villain?"

This.

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I see

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So, can you tell me what makes a good MLP villain?

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Essentially, the same things that would make a good MLP hero, but simply flipped on their head. The villain has to be nuanced enough to feel like a natural person (unless their role is strictly dedicated by the physical aspect of being a challenge that the protag needs to overcome). They need to have actual personality traits that present an entertaining dynamic with the rest of the cast. Maybe their nature could be viewed differently depending on who you ask or maybe they just have a certain style of doing things that makes them stand out from the generic robber, bully, asshole peon, etc. Most of all, a great villain challenges the hero on all levels, not just in terms of power. The very existence of said villain has to be a twisted inversion of what the main hero represents.