The missing thing in Lily's picture is harmony and balance. She sees Mrs. Ramsay as a model since she is painting Mrs. Ramsay. Just like Mrs. Ramsay is always exuding love and trying to create the balance and harmony around her, Lily is trying to do the same in her picture. That's why, as we reach the end of novel, we see that Lily sees Mrs. Ramsay in a vision and she connects her thoughts with the journey of Mr. Ramsay, she draws a line in the middle of her painting and says " I have had my vision." As she sees Mrs. Ramsay in a vision, she becomes one with her, just achieving the essence of Harmony.
Lily's painting is missing the middle. Her painting shows two seperate realms between males and females. Lily can't decide what to put into the middle of the picture and finally just puts a line because she has so much trouble connecting the two realms.