I think Vivi should at least get an honorable mention. He is believed to be a killer because he's a Black Mage, accused dozens of times for crimes he didn't commit, he sees other Black Mages treated like tools and dying left and right...
"My fist is the divine breath. Rise, o fallen seed, and draw upon thy hidden power! Grant upon thee the power of the glorious Mother of Destruction!"
The three people leading are the only right answers. Noel is the last human alive and witness many love one die in harsh conditions. Not to mention he was abandon by his big brother/father figure just before his friend/love interest dies.
Terra was a puppet or slave to a madman for 18 years of her life. I would hate to know what Kefka and the soldiers did to her body when she isn't out killing people. Then there's Cloud. He's the most ****ed up in the head out of any Square MC. Who wouldn't be after going through everything that was thrown at him in his game. Only Fei has him beat in being a head case.