Fay in some ways is exactly what Charlie needed to help him deal with his repressed sexuality. She is certainly not his intellectual match, and their relationship is based in many ways on the fact that he was attracted to her after seeing her in her underwear. Their sexual relationship is somewhat baseless and as soon as he gets too absorbed in his research to pay enough attention to her, she quickly disappears from his life.
Alice in many ways represents the opposite. She is one of the first people in Charlie's life to honestly care about him and to try and help him along his way. Their relationship is somewhat tortuous though, as he falls in love with her, then she pushes him away, then later when the opposite occurs, it is intensely difficult for her to admit that things are not going to work out between them. But she maintains her caring and loving attitude, again contrasting the rather superficial nature of his relationship with Fay.