Is the primary interest of the story in plot, character, theme, or some other element?
I believe that the primary interest of the story "Where Are You Going, Where Have You Been?" is the characterization. However, the plot and the theme are still both powerful elements of the story.
The plot is based upon a true story of three murders in Tuscon, Arizona, in 1966, and this event is eerily infused into Oates' story. The subtle way Connie crosses Arnold Friend's path, which ultimately leads him to her door, sneaks up on the reader. And the end of the story imbues the reader with the overall sense of the unpredictability of life, and dangers that may lie in wait, unseen.
The most outstanding theme may be Connie's vision of the world (one that is a common misconception we have when we are young) that life has nothing to teach us, and that those people who try are out of touch with reality. The truth, however, is that there is never a final answer, and that no matter what we know, there is more to learn—and that when human beings are involved, the outcome of any situation cannot be determined or predicted because human beings are unpredictable creatures.
The characterizations are the most interesting to me. Connie's character is believable and predictable, which is unsettling based on the story's end--she has little regard for the concerns of her mother and feels that she is far beyond her mother's worries and the reality in which her mother exists. It is her total disregard for her mom's experience of the real world that makes her such an easy mark for a predator. Arnold Friend is chillingly portrayed, like a snake waiting to strike—especially in that he is able to so easily and thoroughly mesmerize Connie into submitting to his entreaties so that she leaves the safety of her house and willingly goes with him. The social "savvy" she believes she has is as transparent and useless as a spider web—as she is helpless to resist him, and this is what leads to her death.