I do have a main character who travels with the comic's party of heroes who happens to be an anti-villain. She is the protagonists' opposing force for the first arc, though I'm not sure she can be called an antagonist throughout the rest of the comic. She plays a very central role, and in the comic's second arc/major installment, she temporarily becomes the MC as it delves into her past.
Basically, whether or not she's actually morally-deficient or evil in any sort of way just depends on how the reader feels about her. A sort of "Light Yagami" situation. She is a princess trying to overthrow a Queen of corrupt values, but in doing so kills a lot of people. Her own people have been subject to brutality and segregation under this Queen, so her motives are relatively valid. And she is, at the end of the day, a very sweet and cute character.
The thing that makes her a "Villain" is the fact that the other MC's follow the Queen and are on a mission to save her, thus they form the opposition by default. Which gets kinda sticky because she's actually in love with one of these characters.
Anywho, back to the point. I honestly do kinda root for her even if she's the Villain. I take her side. I think all it takes is some believability and a solid character. Many people adore villains, it's not a surprise some like them as MC's
