I would want to support #3. Clearly, the theme of teaching and learning is essential to the story, and is what stood out most to me, along with the other themes. The narrator shows that, although he is supposedly the expert teacher going to teach his learner, he has a lot to learn about what it is to be a man and his own identity as well. This adds another fascinating dynamic to this tale.
The theme of civil rights and racism is prevalent in the story. One of the points the author makes is that while racism existed between whites and blacks, it existed between blacks and mulattoes as well. Civil rights is the antithesis of racism. Whereas racism pits one perceived superior group against another perceived inferior group, civil rights pits human dignity and respect against ignorance and callousness.
The enotes page on this novel suggests that three major themes are justice vs. injustice; God and religion; and racism. Those are a good start, but I would also add that I think there is an interesting point about teacher vs. learner. In the novel, there is a lesson to be learned before dying and at first it is established that the grandmother wants her young grandson to be educated before he is put to death so that no one can say that he died an ignorant fool. As the novel progresses though, it is clear that the teacher has a few things to learn himself from the experience of working with the young man and dealing with his own life's issues.