Lord of the Flies features four main characters: Ralph, Jack, Piggy, and Simon. Ralph is elected leader by the boys because he appears to have leadership qualities; however, he does not actually have what it takes. Jack was appointed the leader of the choir; however, when the choir gets to choose, they do not choose Jack. Piggy has the best collection of leadership qualities, but because of how he looks no one will follow him. That leaves Simon.
Your question implies that Simon is, in fact, the best leader on the island. Obviously that's not true, since the one time he tries to lead them he is killed. Your follow-up statement mentions leadership qualities, and that's a little different than actually being a leader. Simon is a hard worker, but he is prone to fainting spells. Simon is kind to the littluns when others are not, but he also feels the need to escape to his hideaway quite often.
The one quality which does set him apart as a potential leader is his innate understanding of human nature. If he had been able to make the rest of the boys see it, they may all have survived and even thrived. Instead, no one paid attention. That's not leadership.
Simon is often considered the Christ-figure in this book. If you look throughout chapter 9, you will find that during his struggle, you have many allusions to biblical experiences of the Christ. Regardless of how you think and feel about the biblical character of Jesus Christ, he represents great sacrifice for one's friends. Simon fulfilled this duty to the other boys throughout the book. In chapter 9 you should specifically be able to find quotes that demonstrate Simon possessing knowledge of the truth, struggling to share it, and finally being killed for having it.
Earlier in the book, Simon chooses to join Jack and Ralph to go find the beast (maybe to really prevent them from hurting each other) in chapter 6/7. Simon contributes to building huts and is always a humble messenger to Ralph. No one knew how helpful he really was. For your assignment, you want to assert that this type of sacrificial leadership is better than the others. Read his character profile linked below for quotes, and the style section under the heading of symbolism for understanding the symbol that Simon was.