Elizabeth-Jane isn't the main character of the novel – that role is reserved for her stepfather, Michael Henchard – but she does serve as a kind of moral compass. Her instincts are almost always right, in spite of her lack of formal education. She has a natural intelligence, is righteous without being preachy and beautiful without being flashy. In short, all of her good qualities seem to be the result of nature rather than education or outside influence. And since this is a novel in which being natural and honest is always better than being artificial and deceptive, it makes sense that Elizabeth-Jane, the "flower of nature" (44.7), should be the moral center.
As great as Elizabeth-Jane is, though, she might not be someone you'd want to invite to your next dinner party. She's not very cheerful and she seems to have trouble enjoying herself even after her mother marries Henchard and they have all the money they need:
Knowledge – the result of great natural insight – she did not lack; learning, accomplishments – those, alas, she had not; [. . .] Perhaps, too, her grey, thoughtful eyes revealed an arch gaiety sometimes; but this was infrequent; the sort of wisdom which looked from their pupils did not readily keep company with these lighter moods. Like all people who have known rough times, lightheartedness seemed to her too irrational and inconsequent to be indulged in except as a reckless dram now and then. (14.2)
"Lightheartedness" or cheerfulness is irrational? Yeah, Elizabeth-Jane is kind of a downer. The narrator draws a distinction between "knowledge" and "learning and accomplishments." What is the difference, exactly? Well, her "knowledge" is due entirely to her "natural insight" – her ability to look at the world and draw conclusions and see patterns in the things and people around her. Essentially, it's her natural intelligence. "Learning and accomplishments" are things that would require a formal education – she doesn't know geography or foreign languages, she doesn't play the piano or sing, and she doesn't know the steps to all the formal, popular dances that wealthy young people used to dance at balls.
The narrator seems to want to emphasize that those things – "learning and accomplishments" – are really just superficial. You can add those anytime; you just need a few books and the patience to read them. But "natural insight" is something you're either born with or you're not.
So if Elizabeth-Jane is so great, why aren't all the young men in Casterbridge in love with her? The narrator says that it's because she isn't flashy enough. Your average young man falls in love with flirty girls who wear fashionable clothes and dance at parties, not with the quiet, serious girl who watches from her quiet, serious corner, even if she is the prettiest girl in the room.
Sober and discreet, she was yet so hearty, that her homespun simplicity afforded none of those piquant problems which are afforded by the simplicity that is carefully constructed by art. When she walked abroad she seemed to be occupied with an inner chamber of ideas, and to have slight need for visible objects. (15.1)
Elizabeth-Jane has such an active mind and such a full "inner chamber of ideas" that she always seems preoccupied when people see her. And she's so natural that people don't notice her. She fades into the landscape. By telling us that Elizabeth-Jane has this "inner chamber of ideas," the narrator suggests that there's a real, complicated psychology behind her. She's not just a pretty face, like some other women (ahem, Lucetta), and the narrator seems to want to make her more than just a flat character. He suggests that there's real psychological depth there – an "inner chamber of ideas" beyond what we can see on the page.