Personally, I think Chrysalis makes a better villain than Mr. "Chocolate-filled-cotton-candy-clouds" but I still like him just fine. After all, who else could drink glass and make chocolate milk explode? *actually has an answer to that*
To be fair, Discord isn't a VILLAIN. He's an antagonist. There is a difference.
A VILLAIN is someone who has a plan, goal, or desire that would not only contrast actively with the hero of a story, but be interpreted as "evil" due to the decisions the character chooses to make in order to achieve their goal. Like King Candy in Wreck-it Ralph. He wants to maintain absolute control over the game Sugar Rush, which contrasts with Vanellope's goal to become an official racer, and King Candy is willing to tamper with the game's code (POTENTIALLY endangering the lives of the citizens of Sugar Rush), bar Vanellope from qualifying for racing (not entirely dangerous, but kind of annoying when you have to hide from the police and local bullies), and even attempts to MURDER Vanellope in order to keep her from crossing the finish line!
An ANTAGONIST, on the other hand, is someone who provides opposition to the protagonist, occasionally spurring the protagonist to find a goal for their story and take active measures to see it fulfilled, but is not inherently evil. Like Gene from the same movie. He's not EVIL, per se, and I don't think he was consciously aware of his impact on Ralph. He's just some snobby rich guy who serves as the "final straw" for Ralph, inadvertently sending him on his journey to find some sense of self-worth. He provided opposition, which fueled the action of the story. Or at least the first act, then Sugar Rush and the Cy Bug provided plenty of story propellent.