My favorite villain would have to be Starlight Glimmer, even though I didn't really like the first and last episodes of S5. The fact that she was able to manipulate so many ponies so easily is something that no other villain in MLP has done, which shows that she has extraordinary power beyond her magical abilities, making her story easier to apply in the real world. Another thing that I enjoy about her is that unlike most villains, she didn't start out as a mysterious creature with immense power, but instead as an ordinary unicorn with a gift for magic, which makes her accomplishments even more impressive. Her biggest flaw was her backstory, though there is most likely more to it than what she told Twilight in just two minutes.