Villains bring about a different edge than protagonists do. I think a lot of people found it pretty cool to be able to play as Ganondorf, Mewtwo, and Bowser in Melee, because they're just such different characters. Mewtwo and Ganondorf have their wicked laughs, and Bowser has his deep roars. So on one hand, it's that they offer personality types and character types that we don't really see in protagonists. On the other hand, they offer somewhat different moveset styles as well. Before Bowser, the only real character like him was DK, but even DK was a speedy character. Ganondorf and Wolf were more powerful versions of characters who they are based on (the later only mildly), etc. Villains often have hard-hitting attacks, or use dark/evil magic, or sneaky attacks. For instance, you know who would have been better than a lot of the Fire Emblem cast in this game? Many of its villains.