Though Jude is willing to go against social conventions and to be an individual before he meets Sue, Jude's individuality is considerably less distinct than Sue's individuality.
More than any other character in the novel, Sue finds conformity impossible. She balks, rebels, evades and otherwise avoids conforming to social norms at nearly every turn. Her steadfast and sometimes destructive idiosyncrasy open Sue up to a claim that she is marked by greater obscurity than Jude or Philotson.
In Sue's case, the rules that govern society simply do not fit with her sense of self and her sense of morality. What it right for Sue is often not right for others. Despite her very strong personal inclinations to remain free of marriage, Sue is drawn at times to fulfill social expectations from a woman of her age. This conflict explains why she marries Philotson initially and it is also why she leaves him.
...she marries Phillotson in a tangle of pique, muddle, obligation, and ignorance.
This highly personal and conflicted ethical sense also keeps Sue from marrying Jude and leads her to, effectively, ruin Jude's life.
Truly unable to conform even when she is reluctantly willing, Sue is socially obscure, set apart from the norm by the tenets of her character. Hers is a "unique and painful individuality—at once confused and distinct, fragile and sharply etched..."
These qualities in Sue ultimately obscure her completely, as she attempts to change, to conform, and to do what is expected of her by leaving Jude for Philotson. In this effort, Sue acts against her nature, effectively erasing and nullifiying herself.
When we no longer hear her voice, it is because Sue is alienated from herself as well as us.
No greater obscurity is available than that which Sue experiences as she loses trust in the value of her true character and attempts to replace it with a false one.
The complexity and obscurity of Sue's moral sense is clear in her own words:
What tortures me so much is the necessity of being responsive to this man whenever he wishes, good as he is morally!
Sue feels obligated to play a role as society has defined it, yet is incapable of bringing herself to do so. She is morally driven to be a good wife to Philotson. At the same, she is repelled by the idea of submitting her will, her body, and her identity to a husband.