Very interesting question. Clearly there could be many "common themes," but if I had to answer this question I would want to approach it by considering the power of love and friendship in a hostile world. Both settings of these great novels present the world as set against human relationships. In Of Mice and Men, for instance, we are presented with a world full of rootless, wandering itinerant workers who selfishly look after themselves in an environment of intense poverty and despair. Likewise Santiago populates a world where his luck has gone bad, and he is aged and alone. However, in spite of these settings and the way that fate conspires against them, both novels talk about the redeeming power of friendship and love. Lenny and George are remarkable to the other workers because they travel around together and help and support each other (though clearly George does more supporting than Lennie.) Likewise, Santiago through his relationship with Manolin shows how love and friendship is able to transform us, as Manolin receives affirmation from Santiago that he has never received from his father. Manolin thus supports Santiago and plans to care for him.
In an often indifferent universe, friendship and the bonds of human love show themselves to be powerful and vibrant. This is the theme that I would focus on if I were comparing these two works.