The ideal way to choose a theme is to find some aspect of the story that really interests you. Although a general theme is a good starting point, in a paper for a class you might want to focus closely on some narrower point that illustrates a general theme.
The major theme that dominates the book is that of illusion or surface appearance versus reality. The opera, of course, is a place where illusion is created for entertainment. Not only is there the illusion created on stage, but also there are secret passages and complex stage machinery intended to help create that illusion. While the opera is concerned with illusion, so too is Erik. His deformity masks a clever mind, but eventually his surface appearance transforms his character, creating an ugly interior to match his outward nature.
One theme that might be interesting for your paper is examining how prejudice harms both its perpetrators and its victims. You could ask whether Erik would have become evil if he had not been treated badly by his society. Another possibility might be analysis of the actual machinery used to create illusion in the opera house and the way in which this realistic description of the backstage areas contributes to the effect of the novel.
Some of the many themes in this work include love, appearance vs. reality, good vs. evil, music, and light and dark imagery. Music and love unify the entire piece...all the characters are involved in these two themes. Christine and the Phantom are both involved in appearance vs. reality.
A theme is a unifying idea or aspect in a work. In this instance, the theme of appearance could be explored. The phantom is two different people.When he has his mask on, he is a romantic, tragic hero. He is just in need of attention .
When he takes of the mask, he is anything but a romantic hero, he is hideous, rough, and angry.